├── 00_build_index_hisat2.sh ├── 01_lastz_prepare_kmers.sh ├── CopyNumberGen.sh ├── ExtractSCOs.sh ├── ExtractSeq.sh ├── Fastq2CA.sh ├── GI2Taxonomy.sh ├── GOseq_auto.sh ├── GuessEncoding.sh ├── JRC.sh ├── JobBLAST.sh ├── JobP128.sh ├── JobQ.sh ├── JobR.sh ├── JobR_BLAST.sh ├── JobR_condo.sh ├── JobTime.sh ├── JobTime2.sh ├── Khmer_interleave.sh ├── L3.ModuleGen.sh ├── LAS-makeSLURMp.py ├── Lines_based_file_deletion.sh ├── ModuleGen.sh ├── N50Calc.pl ├── PcB_filter_stats.sh ├── Quiver_01.sh ├── Quiver_02.sh ├── README.md ├── Rscript_for_plotting_bayescan_results.sh ├── Rscripts ├── ElementScript.R ├── Elementsource.R ├── QS.R └── gff2gtf.R ├── SAM_to_sortedBAM.sh ├── SOYGO ├── ANML │ ├── ANML.4Kevin │ ├── ANML.BP.final │ ├── ANML.MF.final │ ├── ANML.list │ ├── ANML.list_BP.txt │ ├── ANML.list_BP_fisher.txt │ ├── ANML.list_BP_names.txt │ ├── ANML.list_BP_out.txt │ ├── ANML.list_BP_output.txt │ ├── ANML.list_ERROR.txt │ ├── ANML.list_MF.txt │ ├── ANML.list_MF_fisher.txt │ ├── ANML.list_MF_names.txt │ ├── ANML.list_MF_out.txt │ ├── ANML.list_MF_output.txt │ └── ANML.list~ ├── ATH_GO_GOSLIM.022714 ├── GOinfoKevinupdate2.pl ├── Gmv2_GODb ├── README_SOYBASE ├── SOYGO.pl ├── Script_Fisher.R ├── SoyGO.sh └── combinefilesbyGO.pl ├── SRAfq2FASTQ.sh ├── a_loghistory_func.sh ├── a_longhistory_func.sh ├── abacas.1.3.1.pl ├── acd_func.sh ├── addFastaHeaders.pl ├── backup ├── bayes_script.sh ├── biostar ├── biostar.cpp ├── blastXML2Tab.py ├── blast_job_gen.sh ├── blast_wrapper.sh ├── bowtie2_se_noclip.sh ├── bwa_map_sort.sh ├── cb ├── cdgit ├── cegma.sh ├── checkBlastStatus.sh ├── clean_trinity.sh ├── combineRawFiles.sh ├── configFiles ├── PcB_subreadfiltering_settings.xml └── vcf_structure.spid ├── connected_graphs.awk ├── count.sh ├── count_fastq.sh ├── create_sam.sh ├── decison_tree_for_picking_common_strata_for_orthogroups.sh ├── dos2unix ├── downloadSRA_ebi.sh ├── edit_sam_files.sh ├── end_time.sh ├── extract_seq.sh ├── extract_seq.sh.save ├── fasta-splitter.pl ├── fasta2fastq.py ├── fastaMulti2singleLine.pl ├── fastaSortByName.pl ├── fasta_distribution.pl ├── fasta_length.py ├── fastarange ├── fastarange.c ├── fastasplitn ├── fastasplitn.c ├── fastq-splitter.pl ├── fastq2fasta.sh ├── fastqc_parse.py ├── fastqc_stats.sh ├── fasttrans ├── fasttrans.c ├── filecount ├── filter_parllel_log.sh ├── firstInstanceOf.awk ├── fna_qual2fastq.py ├── formatOut2Tab.sh ├── fq2bam.sh ├── genome-gaps-as-bed.py ├── get_GitHub_file ├── get_GitHub_file.sh └── get_GitHub_folder.sh ├── get_ip ├── get_taxanomy.sh ├── gff2fasta.pl ├── gitgrep ├── gmap_cdna.sh ├── gsize.sh ├── gsnap_pe.sh ├── gsnap_pe2.sh ├── gsnap_pe_clip.sh ├── gsnap_pe_clip_final.sh ├── gsnap_pe_noclip.sh ├── gsnap_pe_noclip_final.sh ├── gsnap_se.sh ├── gsnap_stats.sh ├── gtf2gff3.pl ├── guess_encoding.py ├── header_replace_fasta.pl ├── histogram.awk ├── htseq_count.sh ├── interleave_PE_fastq.sh ├── intervalBins.awk ├── join.pl ├── join_files.sh ├── joinr.sh ├── khmer_pe.sh ├── mac2unix ├── makeLocalSLURMp.py ├── makeLocalSLURMs.py ├── makeNovaSLURMs.py ├── makePBSp.py ├── makePBSs.py ├── makeSLURM_bridges.py ├── makeSLURMp.py ├── makeSLURMp_ceres.py ├── makeSLURMs.py ├── makeSLURMs_ceres.py ├── mayday.sh ├── md ├── mismatch-counter.sh ├── mpblast.pl ├── nanoVersions.sh ├── newModuleGen.sh ├── new_Assemblathon.pl ├── noTabCompletion.sh ├── numberPatMatch_byLine ├── parse.sh ├── pathadd ├── pb_errc.sh ├── pb_errc2.sh ├── prepare_genome_modules.old ├── qcMarkdownGenerator.sh ├── qiime_config.sh ├── qn ├── qourum_ec.sh ├── quedel.sh ├── readme.md ├── removeRedundantScaffolds.sh ├── removeSeqsFromReads.sh ├── renamed_results.sh ├── reorder_fasta.py ├── rowsums ├── rsem_analyize_dge.sh ├── rsem_dge.sh ├── rsem_estm_matrix.sh ├── runAugustus.sh ├── runBUSCO.sh ├── runBWAcrossspp.sh ├── runBayesScan.sh ├── runBlobtools.sh ├── runBraker.sh ├── runDigiNorm_pe.sh ├── runGenomeScope.sh ├── runGenomeScope_arun.sh ├── runGmap.sh ├── runGuidenceAA.sh ├── runGuidenceNT.sh ├── runHISAT2.sh ├── runIRF.sh ├── runLTRfinder.sh ├── runMaSuRCA.sh ├── runMegablast.sh ├── runMinimap2-cDNA.sh ├── runPlatanus.sh ├── runRAxML.sh ├── runRepeatExplorer.sh ├── runRepeatModeler.sh ├── runSNPHYLO.sh ├── runSOAP.sh ├── runSPAdes.sh ├── runSTAR.sh ├── runSpliceSites.sh ├── runStringtie.sh ├── runSynteny.sh ├── runTabix.sh ├── runTasselGWAS.sh ├── runTraning.sh ├── run_gmap.sh ├── rundipSPAdes.sh ├── sample_fastq.py ├── scaffold2contig.pl ├── scores2dokuwiki.sh ├── seprate_paired_reads.sh ├── soap_config_file.txt ├── split_submit.sh ├── sr_config_MaSuRCA.txt ├── sr_config_MaSuRSOAP.txt ├── star_build.sh ├── sub ├── summary.sh ├── taxadump_gen.sh ├── taxaids2division.sh ├── taxaids2lineage.sh ├── taxid_ranks.py ├── template.slurm ├── test_bioperl.pl ├── tophat_se.sh ├── transpose.awk ├── trim_pe.sh ├── trim_se.sh ├── trimmomatic_pe.sh ├── trimmomatic_se.sh ├── unix2dos ├── unix2mac ├── validate_features.pl ├── vcf-subset.py └── walltime /00_build_index_hisat2.sh: 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