├── README.md └── scripts ├── 1_mapping_sunks ├── KmersPos.py ├── SUNKsharing.py ├── Snakemake.py ├── example_output │ ├── chr8_asat_ONT.kmers │ ├── reads.positions │ ├── reads_nodup.fa │ ├── reads_nodup.fa.fai │ └── shared_SUNKs.tbl ├── kmers.fofn ├── ont_reads.fasta └── runsnake.sh └── 2_tiling ├── SUNKintervals.py └── run_sharedSUNKs.sh /README.md: -------------------------------------------------------------------------------- 1 | This repository contains scripts for the targeted assembly of complex genomic regions using singly unique nucleotide k-mers (SUNKs), or strings of length k that occur once in the genome. The scripts provided here use a SUNK library (i.e. generated with Jellyfish) and a set of ONT reads as input to barcode ONT reads and filter them based on shared SUNKs and their pairwise distances. 2 | 3 | All scripts are designed to run on the Eichler lab cluster and will need to be modified to run on different clusters. 4 | -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/KmersPos.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from Bio import SeqIO # for reading fastq files 3 | import argparse # for writing user-friendly command-line interfaces 4 | import sys 5 | from collections import Counter #for counting # of times a chromosome's kmer is found in the read 6 | import pandas as pd 7 | 8 | parser = argparse.ArgumentParser(description="") 9 | parser.add_argument("-k", "--kmers", help="input unique kmers", type=argparse.FileType('r'), default="/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr6_CCS/25/Illumina_all_count_CCS_chr6_25_91to124.kmer") 10 | parser.add_argument("-fa", "--fasta", help="input fasta file", type=argparse.FileType('r'), default="/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr6_CCS/kmersinONTreads/25mer/test.fasta") 11 | parser.add_argument("-c", "--count", help="min num of kmers in read", type=int, default=1) 12 | parser.add_argument("-o", "--out", help="output fasta (with kmercount in description)", type=argparse.FileType('w'), default=sys.stdout) 13 | parser.add_argument("-p", "--pos", help="output table (readid\tkmer\tpos)", type=argparse.FileType('w'), default="pos.tbl") 14 | args = parser.parse_args() 15 | 16 | # read all kmers into a list 17 | kmers = set() 18 | with args.kmers as f: 19 | for line in f: 20 | kmers.add(line.strip()) 21 | klen = 0 22 | for idx, kmer in enumerate(kmers): 23 | if(idx == 0): 24 | klen = len(kmer) 25 | assert klen == len(kmer), "ERROR: unequal kmer sizes! {} {}".format(klen, len(kmer) ) 26 | 27 | # read in a fasta file 28 | fasta = SeqIO.parse(args.fasta, "fasta") 29 | 30 | # search each line in fasta file for kmer 31 | outrec = [] 32 | outadj = {} 33 | for idx, read in enumerate(fasta): 34 | seq = read.seq 35 | counter = 0 36 | for i in range(len(seq) - len(kmer) + 1): 37 | kmer = seq[i:(i+klen)] 38 | if(str(kmer) in kmers): 39 | counter += 1 40 | if(read.id not in outadj): 41 | outadj[read.id] = set() 42 | outadj[read.id].add( (kmer,i) ) 43 | elif(str(kmer.reverse_complement()) in kmers): 44 | counter += 1 45 | if(read.id not in outadj): 46 | outadj[read.id] = set() 47 | outadj[read.id].add( (kmer.reverse_complement(),i) ) 48 | 49 | 50 | # we need to write the read or not 51 | print("read#:{}\tkmercount:{}".format(idx, counter), file=sys.stderr) 52 | if counter >= args.count: 53 | read.description = read.description + "\tNumber of kmers:{}".format(counter) 54 | outrec.append(read) 55 | 56 | 57 | SeqIO.write(outrec, args.out , "fasta") 58 | 59 | # some code to write out adj to a file 60 | for key in outadj: 61 | if(len(outadj[key]) >= args.count): 62 | 63 | # this makes args.pos 64 | lines = "" 65 | for kmer, pos in outadj[key]: 66 | lines += "{}\t{}\t{}\n".format(key, kmer, pos) 67 | args.pos.write(lines) 68 | 69 | name = args.pos.name 70 | args.pos.close() 71 | df = pd.read_table(name, sep="\t", names=["readid", "kmer", "pos"]) 72 | df.sort_values(by=["readid", "pos"], inplace=True) 73 | df.to_csv(name, index=False, sep="\t", header=False) 74 | 75 | 76 | 77 | -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/SUNKsharing.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from Bio import SeqIO # for reading fastq files 3 | import argparse # for writing user-friendly command-line interfaces 4 | import sys 5 | from collections import Counter #for counting # of times a chromosome's kmer is found in the read 6 | import pandas as pd 7 | 8 | one_read = "/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr8_CCS/kmersinONTreads/leftCen8Read/leftcen8read_trim450kb_20.pos" 9 | other_reads = "/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr8_CCS/kmersinONTreads/20mer/summary/subset_reads_50SUNKsormore.pos" 10 | lens = "/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr8_CCS/kmersinONTreads/leftCen8Read/lengths_of_reads_sharing_SUNKs_20mer.txt" 11 | 12 | parser = argparse.ArgumentParser(description="") 13 | parser.add_argument("-1", "--pos1", help="position table of SUNKs in one read", type=argparse.FileType('r'), default=one_read) 14 | parser.add_argument("-2", "--pos2", help="position table of SUNKs in all other reads", type=argparse.FileType('r'), default=other_reads) 15 | parser.add_argument("-l", "--len", help="lengths of reads other reads", type=argparse.FileType('r'), default=lens) 16 | parser.add_argument("-o", "--out", help="output table (readId1\treadId2\tnumOfSharedSUNKs)", type=argparse.FileType('w'), default=sys.stdout) 17 | args = parser.parse_args() 18 | 19 | # read position table into a dictionary 20 | namedict = {} 21 | kmer_color = {} 22 | posdict = {} 23 | lendict = {} 24 | 25 | with args.len as f: 26 | for line in f: 27 | name, length = line.strip().split() 28 | lendict[name] = int(length) 29 | 30 | def readfile(myfile, first=False): 31 | if(first): 32 | count = 0 33 | 34 | with myfile as f: 35 | for line in f: 36 | name, kmer, pos = line.strip().split() 37 | 38 | # add kmer to set of associated with read name 39 | if(name not in namedict): 40 | namedict[name] = set() 41 | namedict[name].add(kmer) 42 | 43 | # associate a read name and kmer with a position 44 | posdict[(name, kmer)] = pos 45 | 46 | # add a color for the kmer if it is the first read (file) 47 | if(first): 48 | kmer_color[kmer] = count 49 | count += 1 50 | 51 | names = list(namedict.keys()) 52 | return(names) 53 | 54 | oneread = readfile(args.pos1, first=True) 55 | assert len(oneread) == 1, "First argument can only have one read!!!" 56 | 57 | 58 | # add header 59 | form = 8*"{}\t" + "{}\n" 60 | args.out.write(form.format("t_name", "t_len", 61 | "q_name", "q_len", 62 | "shared", 63 | "kmer", "kmer_color", 64 | "t_kmer_pos", "q_kmer_pos")) 65 | 66 | name1 = oneread[0] 67 | other_names = readfile(args.pos2) 68 | other_names.remove(name1) 69 | for name2 in other_names: 70 | # kmers that intersect between read1 and read2 71 | inter = namedict[name1].intersection(namedict[name2]) 72 | num = len(inter) 73 | if(num > 0): 74 | for inter_kmer in inter: 75 | args.out.write( form.format( 76 | name1, lendict[name1], 77 | name2, lendict[name2], 78 | num, 79 | inter_kmer, 80 | kmer_color[inter_kmer], 81 | posdict[(name1, inter_kmer)], 82 | posdict[(name2, inter_kmer)] 83 | ) ) 84 | 85 | 86 | args.out.close() 87 | 88 | 89 | -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/Snakemake.py: -------------------------------------------------------------------------------- 1 | import os 2 | import tempfile 3 | import numpy as np 4 | import pandas as pd 5 | import json 6 | import re 7 | import glob 8 | from pprint import pprint 9 | from Bio import SeqIO 10 | 11 | # 12 | # setup the env for each exacution 13 | # 14 | SNAKEMAKE_DIR = os.path.dirname(workflow.snakefile) 15 | snake_dir = SNAKEMAKE_DIR + "/" 16 | shell.executable("/bin/bash") 17 | #shell.prefix("source %s/env_PSV.cfg; set -eo pipefail; " % SNAKEMAKE_DIR) 18 | shell.prefix("source %s/env_python3.cfg; " % SNAKEMAKE_DIR) 19 | python3 = snake_dir + "env_python3.cfg" 20 | python2 = snake_dir + "env_python2.cfg" 21 | 22 | # 23 | # A little complicated to find the temp dir 24 | # 25 | SSD_TMP_DIR = "/data/scratch/ssd" 26 | if "TMPDIR" in os.environ: 27 | TMPDIR = os.environ['TMPDIR'] 28 | elif "TMPDIR" in config: 29 | TMPDIR = config['TMPDIR'] 30 | elif os.path.exists(SSD_TMP_DIR): 31 | TMPDIR = SSD_TMP_DIR 32 | else: 33 | TMPDIR = tempfile.gettempdir() 34 | 35 | 36 | 37 | lines = open("reads.list").readlines() 38 | reads = [] 39 | for line in lines: 40 | reads.append(line.strip()) 41 | print("Number of reads: {}".format(len(reads))) 42 | IDS = range(0, len(reads)) 43 | 44 | print(len(IDS)) 45 | 46 | wildcard_constraints: 47 | ID="\d+" 48 | 49 | localrules: all, final 50 | 51 | 52 | def ReadsFromNum(wildcards): 53 | #rtn = [] 54 | #for key in wildcards: 55 | # #print(key) 56 | # rtn.append(reads[int(key)]) 57 | rtn = reads[ int( wildcards) ] 58 | return(rtn) 59 | 60 | rule all: 61 | input: "final" 62 | 63 | 64 | 65 | 66 | rule read_pos: 67 | input: 68 | fofn="reads.list", 69 | output: 70 | pos = "pos/{ID}.pos", 71 | params: 72 | cluster=" -l mfree=1G -l h_rt=10:00:00 " 73 | run: 74 | readID = ReadsFromNum(wildcards["ID"]) 75 | print(readID) 76 | shell("source ~/.bashrc; grep {readID} reads_sharing_20mers.pos > {output.pos}" ) 77 | 78 | 79 | rule SUNK_sharing: 80 | input: 81 | pos = "pos/{ID}.pos", 82 | output: 83 | txt = "pos/positions_of_{ID}.txt", 84 | params: 85 | cluster=" -l mfree=2G -l h_rt=128:00:00 -pe serial 1 " 86 | threads: 1 87 | shell: 88 | """ 89 | source ~/modules.sh 90 | /net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr8_CCS/kmersinONTreads/SUNKsharing.py \ 91 | -1 parent_20.pos \ 92 | -2 {input.pos} \ 93 | -l lengths_of_reads_sharing_SUNKs_20mer.txt \ 94 | --out {output.txt} 95 | """ 96 | 97 | rule SUNK_intervals: 98 | input: 99 | txt = "pos/positions_of_{ID}.txt", 100 | output: 101 | intervals = "pos/SUNKintervals_{ID}.tbl", 102 | numbers = "pos/SUNKnums_{ID}.txt", 103 | params: 104 | cluster=" -l mfree=4G -l h_rt=128:00:00 -pe serial 1 " 105 | threads: 1 106 | shell: 107 | """ 108 | source ~/modules.sh 109 | /net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr8_CCS/kmersinONTreads/SUNKintervals.py \ 110 | -t {input.txt} \ 111 | -o {output.intervals} \ 112 | -n {output.numbers} 113 | """ 114 | 115 | rule cat_tables: 116 | input: 117 | txt = expand("pos/positions_of_{ID}.txt", ID=IDS), 118 | intervals = expand("pos/SUNKintervals_{ID}.tbl", ID=IDS), 119 | numbers = expand("pos/SUNKnums_{ID}.txt", ID=IDS), 120 | output: 121 | txt_sum = "summary/positions.txt", 122 | intervals_sum = "summary/SUNKintervals.tbl", 123 | numbers_sum = "summary/SUNKnums.txt" 124 | params: 125 | cluster=" -l mfree=4G -l h_rt=128:00:00 -pe serial 1 " 126 | threads: 1 127 | shell: 128 | """ 129 | cat {input.txt} | grep -v "t_name" > {output.txt_sum} 130 | cat {input.intervals} > {output.intervals_sum} 131 | cat {input.numbers} > {output.numbers_sum} 132 | """ 133 | 134 | rule final: 135 | input: 136 | #numbers=expand("pos/SUNKnums_{ID}.txt", ID=IDS), 137 | #intervals=expand("pos/SUNKintervals_{ID}.tbl", ID=IDS), 138 | numbers_sum = "summary/SUNKnums.txt" 139 | output: 140 | "final" 141 | shell: 142 | """ 143 | touch {output} 144 | """ 145 | 146 | 147 | ''' 148 | #!/bin/bash 149 | mkdir -p reads aln results 150 | 151 | NUM=$1 152 | RUN=$2 153 | FOFN=/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/newanalysis/chm13.fofn 154 | REF=/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/newanalysis/data/Lit_plus_RM2_plus_addLit.bed.fasta 155 | # get the NUMth line from fofn and use that bax file 156 | BAX=$(awk '{ if(NR==$NUM) {print $0} }' $FOFN) 157 | echo $BAX 158 | 159 | # output 160 | FASTQ=reads/$NUM.trimmed.fastq 161 | OUT=aln/$NUM_$RUN.bam 162 | OUT_filt_length=aln/$NUM_$RUN_filt_length.bam 163 | OUT_filt_length_chrom=aln/$NUM_$RUN_filt_length_chrom.bam 164 | RES=results/$NUM_$RUN.txt 165 | RES_filt_length=results/$NUM_$RUN_filt_length.txt 166 | RES_filt_length_chrom=results/$NUM_$RUN_filt_length_chrom.txt 167 | 168 | 169 | if [ ! -f $FASTQ ]; then 170 | echo "Making the fastq from bax" 171 | pls2fasta -trimByRegion $BAX -fastq $FASTQ 172 | fi 173 | 174 | ''' 175 | 176 | 177 | -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/example_output/reads_nodup.fa.fai: -------------------------------------------------------------------------------- 1 | 13bda6ad-8b32-4001-bf43-54a3f13d5e84 465909 57 60 61 2 | e287ef0e-ee8a-43f9-8e75-cc25b1e346ed 351027 473789 60 61 3 | c94b42d9-29a6-4a89-bf0f-914964c3b37a 459876 830724 60 61 4 | 2fccef27-b0b8-4145-8d38-b1d88861033b 615932 1298322 60 61 5 | ca87adff-e87b-4ff4-a9f3-dc3470900516 268296 1924576 60 61 6 | 65e625ad-1384-49dc-8e99-ae95a512bf66 332311 2197401 60 61 7 | 6ff9473e-41cf-493a-985e-f1ddf829d6f0 277817 2535308 60 61 8 | f0a2100a-f758-4e3b-afcb-1a1d1ef04125 180910 2817813 60 61 9 | 9acdc070-246a-4007-b01d-14e3136d90e1 407691 3001796 60 61 10 | 15296908-ec20-4be9-9c80-8e26a5ddd368 305966 3416339 60 61 11 | 96438219-0426-4ca5-bf65-7a62458a5141 447657 3727462 60 61 12 | -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/kmers.fofn: -------------------------------------------------------------------------------- 1 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partaa 2 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partab 3 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partac 4 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partad 5 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partae 6 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partaf 7 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partag 8 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partah 9 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partai 10 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partaj 11 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partak 12 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partal 13 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partam 14 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partan 15 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partao 16 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partap 17 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partaq 18 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partar 19 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partas 20 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partat 21 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partau 22 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partav 23 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partaw 24 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partax 25 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partay 26 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partaz 27 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partba 28 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbb 29 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbc 30 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbd 31 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbe 32 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbf 33 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbg 34 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbh 35 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbi 36 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbj 37 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbk 38 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbl 39 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbm 40 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbn 41 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbo 42 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbp 43 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbq 44 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbr 45 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbs 46 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbt 47 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbu 48 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbv 49 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbw 50 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbx 51 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partby 52 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partbz 53 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partca 54 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcb 55 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcc 56 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcd 57 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partce 58 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcf 59 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcg 60 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partch 61 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partci 62 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcj 63 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partck 64 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcl 65 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcm 66 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcn 67 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partco 68 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcp 69 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcq 70 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcr 71 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcs 72 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partct 73 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcu 74 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcv 75 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcw 76 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcx 77 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcy 78 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partcz 79 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partda 80 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdb 81 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdc 82 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdd 83 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partde 84 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdf 85 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdg 86 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdh 87 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdi 88 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdj 89 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdk 90 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdl 91 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdm 92 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdn 93 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdo 94 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdp 95 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdq 96 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdr 97 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partds 98 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdt 99 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdu 100 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdv 101 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdw 102 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdx 103 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdy 104 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partdz 105 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partea 106 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parteb 107 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partec 108 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parted 109 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partee 110 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partef 111 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parteg 112 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parteh 113 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partei 114 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partej 115 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partek 116 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partel 117 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partem 118 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parten 119 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parteo 120 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partep 121 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parteq 122 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parter 123 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partes 124 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partet 125 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parteu 126 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partev 127 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partew 128 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partex 129 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partey 130 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partez 131 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfa 132 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfb 133 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfc 134 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfd 135 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfe 136 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partff 137 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfg 138 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfh 139 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfi 140 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfj 141 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfk 142 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfl 143 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfm 144 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfn 145 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfo 146 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfp 147 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfq 148 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfr 149 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfs 150 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partft 151 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfu 152 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfv 153 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfw 154 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfx 155 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfy 156 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partfz 157 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partga 158 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgb 159 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgc 160 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgd 161 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partge 162 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgf 163 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgg 164 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgh 165 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgi 166 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgj 167 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgk 168 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgl 169 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgm 170 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgn 171 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgo 172 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgp 173 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgq 174 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgr 175 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgs 176 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgt 177 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgu 178 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgv 179 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgw 180 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgx 181 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgy 182 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partgz 183 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partha 184 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthb 185 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthc 186 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthd 187 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthe 188 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthf 189 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthg 190 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthh 191 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthi 192 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthj 193 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthk 194 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthl 195 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthm 196 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthn 197 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partho 198 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthp 199 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthq 200 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthr 201 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parths 202 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partht 203 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthu 204 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthv 205 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthw 206 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthx 207 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthy 208 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parthz 209 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partia 210 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partib 211 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partic 212 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partid 213 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partie 214 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partif 215 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partig 216 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partih 217 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partii 218 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partij 219 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partik 220 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partil 221 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partim 222 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partin 223 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partio 224 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partip 225 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partiq 226 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partir 227 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partis 228 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partit 229 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partiu 230 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partiv 231 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partiw 232 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partix 233 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partiy 234 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partiz 235 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partja 236 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjb 237 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjc 238 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjd 239 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partje 240 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjf 241 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjg 242 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjh 243 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partji 244 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjj 245 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjk 246 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjl 247 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjm 248 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjn 249 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjo 250 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjp 251 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjq 252 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjr 253 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjs 254 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjt 255 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partju 256 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjv 257 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjw 258 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjx 259 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjy 260 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partjz 261 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partka 262 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkb 263 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkc 264 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkd 265 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partke 266 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkf 267 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkg 268 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkh 269 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partki 270 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkj 271 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkk 272 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkl 273 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkm 274 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkn 275 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partko 276 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkp 277 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkq 278 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkr 279 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partks 280 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkt 281 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partku 282 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkv 283 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkw 284 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkx 285 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partky 286 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partkz 287 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partla 288 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlb 289 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlc 290 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partld 291 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partle 292 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlf 293 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlg 294 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlh 295 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partli 296 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlj 297 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlk 298 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partll 299 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlm 300 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partln 301 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlo 302 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlp 303 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlq 304 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlr 305 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partls 306 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlt 307 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlu 308 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlv 309 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlw 310 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlx 311 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partly 312 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partlz 313 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partma 314 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmb 315 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmc 316 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmd 317 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partme 318 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmf 319 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmg 320 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmh 321 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmi 322 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmj 323 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmk 324 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partml 325 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmm 326 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmn 327 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmo 328 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmp 329 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmq 330 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmr 331 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partms 332 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmt 333 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmu 334 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmv 335 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmw 336 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmx 337 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmy 338 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partmz 339 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partna 340 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnb 341 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnc 342 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnd 343 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partne 344 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnf 345 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partng 346 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnh 347 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partni 348 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnj 349 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnk 350 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnl 351 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnm 352 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnn 353 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partno 354 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnp 355 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnq 356 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnr 357 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partns 358 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnt 359 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnu 360 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnv 361 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnw 362 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnx 363 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partny 364 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partnz 365 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoa 366 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partob 367 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoc 368 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partod 369 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoe 370 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partof 371 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partog 372 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoh 373 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoi 374 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoj 375 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partok 376 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partol 377 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partom 378 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/parton 379 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoo 380 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partop 381 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoq 382 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partor 383 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partos 384 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partot 385 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partou 386 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partov 387 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partow 388 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partox 389 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoy 390 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partoz 391 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpa 392 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpb 393 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpc 394 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpd 395 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpe 396 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpf 397 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpg 398 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partph 399 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpi 400 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpj 401 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpk 402 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpl 403 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpm 404 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpn 405 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpo 406 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpp 407 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpq 408 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpr 409 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partps 410 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpt 411 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpu 412 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpv 413 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpw 414 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpx 415 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpy 416 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partpz 417 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqa 418 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqb 419 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqc 420 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqd 421 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqe 422 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqf 423 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqg 424 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqh 425 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqi 426 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqj 427 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqk 428 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partql 429 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqm 430 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqn 431 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqo 432 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqp 433 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqq 434 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqr 435 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqs 436 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqt 437 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqu 438 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqv 439 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqw 440 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqx 441 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqy 442 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partqz 443 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partra 444 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partrb 445 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partrc 446 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partrd 447 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partre 448 | /net/eichler/vol26/home/glogsdon/papers/chm13_hifi_assembly/nobackups/jellyfish/illumina_split_kmers/partrf 449 | -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/runsnake.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" 3 | #source $DIR/env_python3.cfg 4 | module load anaconda/201710 5 | source ~/modules.sh 6 | 7 | # snakemake paramenters 8 | # 9 | snakefile=$DIR/Snakemake.py 10 | jobNum=100 11 | waitTime=60 # this really needs to be 60 on our cluster :( 12 | retry=0 # numer of times to retry the pipeline if it failes 13 | # I allow a retry becuase sometimes even the really long waittime is not enough, 14 | # and the files are actaully there 15 | 16 | # 17 | # QSUB parameters, these are only the defualts, they can be changed with params.sge_opts 18 | # Allow snakemake to make directories, I think it slows things down when I done with "waitTime" 19 | # 20 | logDir=logs 21 | mkdir -p $logDir 22 | E=$logDir'/snakejob_{rule}_{wildcards}_e' 23 | O=$logDir'/snakejob_{rule}_{wildcards}_o' 24 | ram=4G 25 | defaultCores=1 26 | 27 | # 28 | # run snakemake 29 | # 30 | snakemake -p \ 31 | -s $snakefile \ 32 | --drmaa " -P eichlerlab \ 33 | -q eichler-short.q \ 34 | -l h_rt=24:00:00 \ 35 | -l mfree=$ram \ 36 | -V -cwd -e $E -o $O \ 37 | {params.cluster} \ 38 | -l centos=7 \ 39 | -w n -S /bin/bash" -w 60 \ 40 | --jobs $jobNum \ 41 | --latency-wait $waitTime \ 42 | --restart-times $retry \ 43 | $1 $2 # just a way to pass aditional arguments to snakemake, like --unlock 44 | 45 | 46 | -------------------------------------------------------------------------------- /scripts/2_tiling/SUNKintervals.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from Bio import SeqIO # for reading fastq files 3 | import argparse # for writing user-friendly command-line interfaces 4 | import sys 5 | from collections import Counter #for counting # of times a chromosome's kmer is found in the read 6 | import pandas as pd 7 | import glob 8 | import itertools 9 | import csv 10 | 11 | parser = argparse.ArgumentParser(description="") 12 | parser.add_argument("-t", "--table", help="SUNKsharing.py outfile", type=argparse.FileType('r'), default="/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/kmerAnalysis/chr8_CCS/kmersinONTreads/leftCen8Read/positions_of_SUNKs_within_leftcen8readtrim450kb_and_other_reads_20mer.txt") 13 | parser.add_argument("-o", "--out", help="output table (queryId\tSUNK_pair_id\tquery_dist\ttarget_dist)", type=argparse.FileType('w'), default="") 14 | parser.add_argument("-n", "--num", help="number of shared SUNKs (queryId:num_of_shared_SUNKs)", type=argparse.FileType('w'), default="") 15 | args = parser.parse_args() 16 | 17 | # this is a function to determine similarity in distance between query and target SUNKs 18 | # currently, it is set to 1% difference in distance and distance >20 (removes neighboring SUNKSs) 19 | def is_similar(dist_query, dist_target): 20 | diff = abs(dist_query-dist_target) 21 | return (1.0*diff/(dist_target) <=0.01) and (diff>20) 22 | 23 | #read in df 24 | df = pd.read_table(args.table) 25 | 26 | unique_query_reads = list(df['q_name'].unique()) 27 | query_df = df[df['q_name']==unique_query_reads[0]] 28 | 29 | sunkid_position = [] 30 | for idx, row in query_df.iterrows(): 31 | sunkid_position.append((row['kmer_color'], row['q_kmer_pos'])) 32 | 33 | sunkid_pairs = itertools.product(sunkid_position, sunkid_position) 34 | 35 | target_df = df[['t_name', 'kmer_color', 't_kmer_pos']].drop_duplicates() 36 | 37 | #map query reads, their unique pairs of SUNKs, and their corresponding distances 38 | query_sunk_pair_mapping = {} 39 | for query_read in unique_query_reads: 40 | query_df = df[df['q_name']==query_read] 41 | sunkid_position = [] 42 | for idx, row in query_df.iterrows(): 43 | sunkid_position.append((row['kmer_color'], row['q_kmer_pos'])) 44 | 45 | sunkid_pairs = itertools.product(sunkid_position, sunkid_position) 46 | sunk_pair_dist = {} 47 | for pairs in sunkid_pairs: 48 | sunkid_a = pairs[0][0] 49 | sunkid_b = pairs[1][0] 50 | sunk_a_pos = pairs[0][1] 51 | sunk_b_pos = pairs[1][1] 52 | if sunkid_a != sunkid_b: 53 | sunk_pair_list = sorted([sunkid_a, sunkid_b]) 54 | sunk_pair_id = '-'.join(map(str,sunk_pair_list)) 55 | #str(sunkid_a) + '-' + str(sunkid_b) 56 | if sunk_pair_id not in sunk_pair_dist: 57 | sunk_pair_dist[sunk_pair_id] = set() 58 | sunk_pair_dist[sunk_pair_id].add(abs(sunk_a_pos - sunk_b_pos)) 59 | 60 | query_sunk_pair_mapping[query_read] = sunk_pair_dist 61 | 62 | #query_sunk_pair_mapping 63 | 64 | #map target reads, their unique pairs of SUNKs, and their corresponding distances 65 | target_sunkid_position = [] 66 | for idx, row in target_df.iterrows(): 67 | target_sunkid_position.append((row['kmer_color'], row['t_kmer_pos'])) 68 | 69 | target_sunkid_pairs = itertools.product(target_sunkid_position, target_sunkid_position) 70 | target_sunk_pair_dist = {} 71 | for pairs in target_sunkid_pairs: 72 | sunkid_a = pairs[0][0] 73 | sunkid_b = pairs[1][0] 74 | sunk_a_pos = pairs[0][1] 75 | sunk_b_pos = pairs[1][1] 76 | if sunkid_a != sunkid_b: 77 | sunk_pair_list = sorted([sunkid_a, sunkid_b]) 78 | sunk_pair_id = '-'.join(map(str,sunk_pair_list)) 79 | #str(sunkid_a) + '-' + str(sunkid_b) 80 | if sunk_pair_id not in target_sunk_pair_dist: 81 | target_sunk_pair_dist[sunk_pair_id] = set() 82 | target_sunk_pair_dist[sunk_pair_id].add(abs(sunk_a_pos - sunk_b_pos)) 83 | 84 | #target_sunk_pair_dist 85 | 86 | #want to print this as args.out 87 | 88 | matching_query_results = [] 89 | with args.out as f: 90 | for query in query_sunk_pair_mapping: 91 | q_t_keys_intersect = set(query_sunk_pair_mapping[query].keys()).intersection(target_sunk_pair_dist.keys()) 92 | for sunk_pair_intersect in q_t_keys_intersect: 93 | if is_similar(list(query_sunk_pair_mapping[query][sunk_pair_intersect])[0], 94 | list(target_sunk_pair_dist[sunk_pair_intersect])[0]): 95 | args.out.write(("{}\t{}\t{}\t{}\n".format(query, sunk_pair_intersect, query_sunk_pair_mapping[query][sunk_pair_intersect], target_sunk_pair_dist[sunk_pair_intersect]))) 96 | matching_query_results.append((query, 97 | sunk_pair_intersect, 98 | query_sunk_pair_mapping[query][sunk_pair_intersect], 99 | target_sunk_pair_dist[sunk_pair_intersect])) 100 | 101 | 102 | #matching_query_results 103 | #len(matching_query_results) 104 | 105 | # 106 | query_unique_matched_pair_count = {} 107 | for query_kmer_pair in matching_query_results: 108 | if query_kmer_pair[0] not in query_unique_matched_pair_count: 109 | query_unique_matched_pair_count[query_kmer_pair[0]]=set() 110 | query_unique_matched_pair_count[query_kmer_pair[0]].add(query_kmer_pair[1]) 111 | 112 | #want to print this as args.num 113 | 114 | #query_unique_matched_pair_count_final = {} 115 | with args.num as f: 116 | for query_kmer_pair in query_unique_matched_pair_count: 117 | if len(query_unique_matched_pair_count[query_kmer_pair]) > 1: 118 | #query_unique_matched_pair_count_final[query_kmer_pair] = len(query_unique_matched_pair_count[query_kmer_pair]) 119 | args.num.write("{}:{}\n".format(query_kmer_pair, len(query_unique_matched_pair_count[query_kmer_pair]))) 120 | 121 | #query_unique_matched_pair_count_final 122 | -------------------------------------------------------------------------------- /scripts/2_tiling/run_sharedSUNKs.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e # terminate script if command exits with a nonzero exit status 3 | set -u # abort script if a variables value is unset 4 | set -o pipefail # return nonzero exit status if any program in a pipe returns nonzero exit status 5 | 6 | 7 | ######### User-defined parameters 8 | parentRead='13bda6ad-8b32-4001-bf43-54a3f13d5e84' 9 | parentDir='/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/mapping_SUNKs/tiling_across_centromere/demo' 10 | allReads='/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/mapping_SUNKs/tiling_across_centromere/demo/mapping_sunks/summary/reads_nodup.fa' 11 | sharedSUNKsDir='/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/mapping_SUNKs/tiling_across_centromere/demo/mapping_sunks/summary/shared_SUNKs.tbl' 12 | readsPosition='/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/mapping_SUNKs/tiling_across_centromere/demo/mapping_sunks/summary/reads.positions' 13 | kmers='/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/mapping_SUNKs/tiling_across_centromere/demo/mapping_sunks/summary/chr8_asat_ONT.kmers' 14 | cutoff='100' 15 | readLength='100' 16 | 17 | #make the directory 18 | echo "Making the directory" 19 | cd ${parentDir} 20 | mkdir ${parentRead} 21 | 22 | #get the parent read fasta 23 | echo "Getting the parent read fasta" 24 | cd ${parentRead} 25 | /net/eichler/vol26/home/glogsdon/software/seqfilter/seqfilter -i ${allReads} -l <(printf "${parentRead}\n") -o ./${parentRead}.fa 26 | source /net/eichler/vol26/home/glogsdon/modules.sh 27 | samtools faidx ${parentRead}.fa 28 | echo "Parent read retrieved" 29 | 30 | #retrieving shared SUNK file 31 | mkdir SUNKs 32 | source /net/eichler/vol26/home/glogsdon/modules.sh 33 | echo "Identifying SUNKs within read" 34 | /net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/mapping_SUNKs/tiling_across_centromere/KmersPos.py -k ${kmers} -fa ${parentRead}.fa -o SUNKs/${parentRead}.fa -t SUNKs/${parentRead}_20.tbl --pos SUNKs/${parentRead}_20.pos 35 | 36 | echo "Number of reads sharing SUNKs: \ 37 | `grep -c "${parentRead}" ${sharedSUNKsDir}`" 38 | 39 | echo "Generating data for histogram" 40 | grep "${parentRead}" ${sharedSUNKsDir} | sort -rnk3,3 > SUNKs/${parentRead}_sharedSUNKs_20mer.tbl 41 | awk '{print $3}' SUNKs/${parentRead}_sharedSUNKs_20mer.tbl > SUNKs/${parentRead}_sharedSUNKs_20mer.count 42 | echo "Histogram data generated. Data is located here: 43 | `readlink -f SUNKs/${parentRead}_sharedSUNKs_20mer.count`" 44 | 45 | #run repeatmasker 46 | mkdir repeatmasker 47 | module load perl/5.14.2 48 | module load RepeatMasker/3.3.0 49 | RepeatMasker \ 50 | -species human \ 51 | -e wublast \ 52 | -dir ${parentDir}/${parentRead}/repeatmasker \ 53 | -pa 24 \ 54 | ${parentDir}/${parentRead}/${parentRead}.fa 55 | awk '{$16=""; print $0}' repeatmasker/${parentRead}.fa.out > repeatmasker/${parentRead}.fa.15.out 56 | 57 | 58 | #make the SUNK sudirectory 59 | echo "Making the SUNK subdirectory" 60 | cd ${parentDir}/${parentRead}/SUNKs 61 | rm -rf ${cutoff}_or_more 62 | mkdir ${cutoff}_or_more 63 | 64 | #retrieve the read IDs of those with SUNKs greater than the cut-off 65 | echo "Retrieving the reads" 66 | awk '$3 >= 100' ${parentRead}_sharedSUNKs_20mer.tbl | awk '{print $1}' > ${cutoff}_or_more/reads_sharing_20mers_with_${parentRead}.tmp.txt 67 | awk '$3 >= 100' ${parentRead}_sharedSUNKs_20mer.tbl | awk '{print $2}' >> ${cutoff}_or_more/reads_sharing_20mers_with_${parentRead}.tmp.txt 68 | cat ${cutoff}_or_more/reads_sharing_20mers_with_${parentRead}.tmp.txt | sort | uniq > ${cutoff}_or_more/reads_sharing_20mers_with_${parentRead}.txt 69 | echo "k-mer cut-off: ${cutoff}" 70 | echo "read length cut-off: ${readLength}" 71 | echo "Number of reads sharing SUNKs: `wc -l ${cutoff}_or_more/reads_sharing_20mers_with_${parentRead}.txt`" 72 | 73 | #determine the lengths of the reads 74 | grep "${parentRead}" ${parentDir}/${parentRead}/${parentRead}.fa.fai | awk 'BEGIN{OFS="\t"}{print $1,$2}' > ${cutoff}_or_more/lengths_of_reads_sharing_SUNKs_20mer.txt 75 | grep -f ${cutoff}_or_more/reads_sharing_20mers_with_${parentRead}.txt ${allReads}.fai | awk 'BEGIN{OFS="\t"}{print $1,$2}'>> ${cutoff}_or_more/lengths_of_reads_sharing_SUNKs_20mer.txt 76 | 77 | #take only reads above above a certain size 78 | awk '$2 >= 100000' ${cutoff}_or_more/lengths_of_reads_sharing_SUNKs_20mer.txt > ${cutoff}_or_more/lengths_of_${readLength}kb_reads_sharing_SUNKs_20mer.txt 79 | echo "Number of reads above ${readLength} kbp: `wc -l ${cutoff}_or_more/lengths_of_${readLength}kb_reads_sharing_SUNKs_20mer.txt`" 80 | 81 | #filter the pos file 82 | echo "Filtering the pos file" 83 | awk '{print $1}' ${cutoff}_or_more/lengths_of_${readLength}kb_reads_sharing_SUNKs_20mer.txt > ${cutoff}_or_more/${readLength}kb_reads_sharing_SUNKs_20mer.txt 84 | grep -f ${cutoff}_or_more/${readLength}kb_reads_sharing_SUNKs_20mer.txt ${readsPosition} > ${cutoff}_or_more/${readLength}kb_reads_sharing_20mers_with_${parentRead}.pos 85 | 86 | #copy files into the snakemake directory 87 | echo "Preparing the snakemake directory" 88 | mkdir ${cutoff}_or_more/snakemake_for_SUNK_intervals 89 | cp /net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/mapping_SUNKs/tiling_across_centromere/demo/scripts/* ${cutoff}_or_more/snakemake_for_SUNK_intervals/ 90 | 91 | #change the files in the snakemake 92 | cd ${parentDir}/${parentRead}/SUNKs/${cutoff}_or_more/ 93 | cp ${readLength}kb_reads_sharing_SUNKs_20mer.txt snakemake_for_SUNK_intervals/reads.list 94 | grep -v "${parentRead}" snakemake_for_SUNK_intervals/reads.list > temp && mv temp snakemake_for_SUNK_intervals/reads.list 95 | cp ../${parentRead}_20.pos snakemake_for_SUNK_intervals/parent_20.pos 96 | cp ${readLength}kb_reads_sharing_20mers_with_${parentRead}.pos snakemake_for_SUNK_intervals/reads_sharing_20mers.pos 97 | cp lengths_of_${readLength}kb_reads_sharing_SUNKs_20mer.txt snakemake_for_SUNK_intervals/lengths_of_reads_sharing_SUNKs_20mer.txt 98 | 99 | #run the snakemake 100 | cd snakemake_for_SUNK_intervals/ 101 | ./runsnake.sh 102 | cd summary 103 | echo "Files are ready!" 104 | readlink -f positions.txt 105 | readlink -f SUNKintervals.tbl 106 | cat SUNKnums.txt 107 | 108 | 109 | --------------------------------------------------------------------------------