├── .gitattributes ├── 00_assembly └── ONT_original │ ├── 01_1_mapont │ └── mapont │ ├── 01_2_mappb │ └── mappb │ ├── 01_change_contig_name.sh │ ├── 02_1_get_read_depth_ont │ ├── 01_run_get_readdepth.sh │ ├── 02_1kb_window_depth.sh │ ├── draw_abnormal_region │ │ ├── 01_10_gaps │ │ │ ├── 01_get_read_depth.sh │ │ │ ├── 02_draw.sh │ │ │ ├── 03_changename.sh │ │ │ ├── 10Gaps.bed │ │ │ ├── 10Gaps.bed.sorted │ │ │ └── plot_v2.R │ │ ├── 02_13_read_depth_ab_regions │ │ │ ├── 01_get_read_depth.sh │ │ │ ├── 02_draw.sh │ │ │ ├── 03_changename.sh │ │ │ └── plot_v2.R │ │ └── 03_1_inversion │ │ │ ├── 01_get_read_depth.sh │ │ │ ├── 02_draw.sh │ │ │ ├── 03_changename.sh │ │ │ └── plot_v2.R │ ├── get_mapped_bed.pl │ └── make_1kb_depth_line.pl │ ├── 02_2_get_read_depth_pb │ ├── 01_run_get_readdepth.sh │ ├── 02_1kb_window_depth.sh │ └── get_mapped_bed.pl │ ├── 03_1_draw_read_depth_ont │ ├── 01_run_draw.sh │ ├── 02_draw_abnormal.sh │ ├── drawContigDepth.pl │ ├── drawContigDepthLine.pl │ ├── drawContigDepthLineAB.pl │ └── find_abnormal_region_depth.pl │ ├── 03_2_draw_read_depth_pb │ ├── 01_run_draw.sh │ ├── 02_draw_abnormal.sh │ ├── drawContigDepth.pl │ ├── drawContigDepthLine.pl │ ├── drawContigDepthLineAB.pl │ └── find_abnormal_region_depth.pl │ ├── 04_hifiasm_close_5_gap │ ├── 01_change_paf_and_hl.sh │ ├── 02_cp.sh │ ├── 03_linkview.sh │ ├── 04_draw_depth.sh │ ├── changeContigNameHl.pl │ ├── changeContigNamePaf.pl │ ├── drawContigDepth.pl │ ├── drawContigDepthLine.pl │ └── origin_gap.bed │ ├── 05_compare_with_old_Mo17 │ ├── 01_map_to_old_mo17.sh │ ├── 02_draw.sh │ └── draw_chromosome_align.pl │ ├── 06_check_cutoff │ └── 01_map_hifiasm_to_ont_origin_asm.sh │ ├── 07_show_readDepth_Ab_region │ ├── 01_draw_read_depth │ │ ├── 02_draw_abnormal_region.sh │ │ └── drawContigDepth.pl │ ├── 01_generate_anno.sh │ ├── 02_show_hifiasm_map │ │ ├── 01_prepare_paf.sh │ │ ├── 02_draw_linkview.sh │ │ └── k │ ├── 03_show_mapping_read │ │ ├── 01_map_reads.sh │ │ ├── 02_get_files_for_draw.sh │ │ ├── draw_mapping.pl │ │ └── get_mapped_alignment.pl │ ├── 04_show_more_mapping_read │ │ ├── 01_find_theRegion_read.sh │ │ ├── 02_get_region_read.sh │ │ ├── 03_get_fasta_and_len.sh │ │ ├── 04_map.sh │ │ ├── 05_anno.sh │ │ ├── 06_get_infor.sh │ │ ├── 07_get_files_for_draw.sh │ │ ├── 08_run_draw.sh │ │ ├── draw_mapping.pl │ │ ├── get_mapped_alignment.pl │ │ ├── get_mapped_bed.pl │ │ └── get_mapped_infor.pl │ ├── abnormal.show.bed │ └── changeContigNameHl.pl │ ├── 08_estimate_genome_size │ ├── 01_jellyfish.sh │ └── kmer_hist.tsv │ ├── 09_map_ont_pb_asm │ ├── 01_1_map_hifiasm.sh │ ├── 01_2_map_canu.sh │ ├── 02_1_anno_pb_asm.sh │ ├── 02_2_anno_pb_asm.sh │ ├── 02_3_anno_pb_asm.sh │ ├── 02_anno_pb_asm │ ├── 02_show_pacbio_alignment │ │ ├── 01_1_map_hifiasm.sh │ │ ├── 01_2_map_canu.sh │ │ └── 01_map_pacbio_asm.sh │ ├── 03_convert_paf_to_linkview_and_draw.sh │ └── k │ ├── 10_check_SSR_genotype │ ├── 01_find_theRegion_read.sh │ ├── 02_get_region_read.sh │ ├── 03_get_fasta_and_len.sh │ ├── 04_map.sh │ ├── 05_anno.sh │ ├── 06_get_infor.sh │ ├── 07_get_files_for_draw.sh │ ├── 08_run_draw.sh │ ├── draw_mapping.pl │ ├── get_mapped_alignment.pl │ ├── get_mapped_bed.pl │ ├── get_mapped_infor.pl │ └── region.bed.sorted │ └── changeContigName.pl ├── 01_evalue_TAG ├── ONT │ ├── 01_resecue_failed_reads │ │ ├── 01_convert_fq2fa.sh │ │ └── 02_filter_fail_read.sh │ ├── 02_checkB50 │ │ ├── 03_N50.sh │ │ ├── 04_statistic.sh │ │ └── cal_contig_or_scaffolds_n50_GC.pl │ └── 03_over150K_fail_read │ │ ├── 01_extract_150k_reads.sh │ │ ├── 03_combine_anno.sh │ │ ├── 04_read_stat.sh │ │ ├── 05_draw_bigSSR.sh │ │ ├── 07_extract_100_150k_reads.sh │ │ ├── 150K以上fail_read_10K以上SSR_ratio.xlsx │ │ ├── bigSSR.py │ │ └── drop.list ├── PB │ ├── 01_cal_ssr_readlen_ratio.sh │ ├── 02_draw_reads.sh │ ├── 03_map_reads_to_gap.sh │ ├── drawContigRepeat.pl │ ├── find_over10kTAG.pl │ └── list ├── PCRFree │ └── 01_map_reads_to_TAG.sh ├── onlyForGap.xlsx └── recalPB │ └── 01_bam2fastq.sh ├── 02_fill_gap ├── 01_rDNA │ ├── 01_extract_reads_asm.sh │ ├── 02_anno.sh │ ├── 03_map.sh │ ├── concate_seq.py │ ├── fill.list │ ├── fill.tab │ └── other_LTR分析.pptx ├── 02_5Gaps │ └── fill_path ├── 03_telomere │ └── 02_show_read_in_chr2_start │ │ ├── 01_find_theRegion_read.sh │ │ ├── 02_get_region_read.sh │ │ ├── 03_get_fasta_and_len.sh │ │ ├── 04_cat.sh │ │ ├── 05_anno.sh │ │ ├── 06_get_infor.sh │ │ ├── 07_get_files_for_draw.sh │ │ ├── 08_run_draw.sh │ │ ├── draw_mapping.pl │ │ ├── get_mapped_alignment.pl │ │ ├── get_mapped_bed.pl │ │ └── get_mapped_infor.pl ├── 04_TAG │ ├── 01_seqkit_and_map.sh │ └── material.list ├── 05_overall_fill │ ├── 01_read_map.sh │ ├── 03_map_to_check.sh │ ├── 04_5SrRNA.sh │ ├── do_concate_assembly.sh │ ├── estimate_5SrRNA_size │ │ ├── 01_get_read_region.sh │ │ ├── count_Illumina_length.pl │ │ ├── get_the_detailed_mapping_information_from_bwa_bam_file.pl │ │ ├── make_ONT_db.sh │ │ ├── map.sh │ │ ├── map2.sh │ │ ├── run_blast_ont.sh │ │ └── run_blast_pb.sh │ ├── overall_fillpath.sh │ └── read.list ├── 07_polished_region │ ├── 05_draw_telomere.sh │ ├── 06_anno_telomere_read.sh │ ├── drawRepeatInAnyRegion.pl │ ├── telomere.bed │ ├── telomere_reads.len │ └── telomere_to_polish.bed ├── 08_final_fill │ ├── 01_do_concate_assembly.sh │ ├── 02_map_polish_region.sh │ ├── 03_sub_polish_to_final.sh │ ├── 04_split.sh │ ├── 05_anno │ ├── 06_map_to_check_filling.sh │ ├── 07_anno_fill.sh │ ├── 08_combine_anno.sh │ ├── 09_draw.sh │ ├── TAG_piers.fa.len-1.pdf │ ├── region1.k │ ├── region10.k │ ├── region11.k │ ├── region12.k │ ├── region13.k │ ├── region14.k │ ├── region15.k │ ├── region16.k │ ├── region17.k │ ├── region18.k │ ├── region2.k │ ├── region3.k │ ├── region4.k │ ├── region5.k │ ├── region6.k │ ├── region7.k │ ├── region8.k │ ├── region9.k │ ├── telomere.bed-1.svg │ └── telomere_reads.len-1.svg └── 09_check_read_depth │ ├── 01_run_get_readdepth.sh │ ├── 02_1kb_window_depth.sh │ ├── 03_draw_genome_depth.sh │ ├── 04_find_abnormal_region.sh │ ├── 05_10Gaps_draw.sh │ ├── 06_change_name.sh │ ├── Final_10Gaps.bed │ ├── Final_13Coverage.bed │ ├── Final_1Inver.bed │ ├── get_mapped_bed.pl │ ├── make_1kb_depth_line.pl │ ├── mapont │ ├── plot_v2.R │ └── plot_v3.R ├── 03_check_otherLTR ├── 01_find_theRegion_read.sh ├── 02_get_region_read.sh ├── 03_get_fasta_and_len.sh ├── 04_cat.sh ├── 05_anno.sh ├── 06_check_mapped_or_other.sh ├── 07_check_mapping_pos.sh ├── 08_find_reads_mapped_quality.sh ├── check_mapping_pos.pl ├── get_mapped_bed.pl └── get_mapped_quality.pl ├── 04_check_satellite ├── 01_grep_satellite_region.sh ├── 02_find_reliable.sh ├── 03_extract_positive.sh ├── 04_combine.sh ├── generate_monomer.pl ├── run_sd └── upper.sh ├── README.md ├── Step1_Gapfilling ├── 01_QVscore │ ├── HifiaSm组装的长度与merqueryQV值.xlsx │ ├── Mo17.p_ctg.fa.fai │ ├── mo17_hifiasm_merqury.Mo17.p_ctg.qv │ └── mo17_hifiasm_merqury.qv ├── 03_hifiasm_contigs_to_replace │ ├── .vscode │ │ └── settings.json │ ├── 01_map_hifiasm_to_ont_origin_asm.sh │ ├── 02_bedtools_makewindows.sh │ ├── 03_make_k.sh │ ├── mk_karyotype.pl │ ├── ptg000004l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000006l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000008l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000013l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000031l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000038l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000046l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000047l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000059l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000134l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ ├── ptg000148l │ │ ├── query.bed │ │ ├── query.bed.1MB.bed │ │ ├── ref.bed │ │ └── ref.bed.1MB.bed │ └── run_draw_linkview.sh ├── ReadsEvalueSsrSize │ ├── 01_combine_ref_and_map.sh │ ├── 02_find_mapped_reads.sh │ ├── 03_prepare_mapFile.sh │ ├── 04_run_draw.sh │ ├── 05_check_chr4.sh │ ├── generate_mapping_files.pl │ ├── prepare_for_draw_mapping.pl │ └── special.bed ├── extend_by_identifier │ ├── README.md │ └── Step3_redo_transcode_length_to_seq │ │ ├── 01_run_transcode.sh │ │ ├── 03_run_findSecondAlignment.sh │ │ ├── 04_run_draw.sh │ │ ├── draw_rDNA_coor.pl │ │ ├── findSecondAlignment.pl │ │ ├── get_map_correlation.pl │ │ └── sort_reads_and_id.pl ├── filled5Gaps │ ├── 01_run_map.sh │ ├── 02_deal_and_draw.sh │ ├── 06_prepare_draw_file.sh │ ├── 07_draw.sh │ ├── 5个已填gap的reads比对.zip │ └── chr6.k ├── find_bigSSR_genomeRegion │ ├── mapped_pacbio_TAG_reads │ │ ├── 01_scan_window_check.sh │ │ ├── 02_extract_TAG_region.sh │ │ ├── 03_seqkit.sh │ │ ├── 04_anno.sh │ │ ├── extrack_location_reads.pl │ │ ├── extract_type.pl │ │ ├── find_over10kTAG.pl │ │ └── ssr │ │ │ ├── 02_extract_TAG_region.sh │ │ │ └── extract_reads.sh │ └── maskTAG │ │ ├── 01_mask_seq.sh │ │ ├── 02_extract_reads.sh │ │ ├── 03_anno.sh │ │ ├── 04_convert_to_bed.sh │ │ ├── end_extend.py │ │ ├── map │ │ └── mask.pl ├── gapEnd │ ├── 01_run_generate_and_draw.sh │ └── generate_mapping_files.pl └── testDepthAbnormalRegion │ ├── 01_map_pacbio_to_contig.sh │ ├── 02_draw.sh │ ├── 5_204_205M.list │ ├── anno │ ├── canu.bed │ ├── canu.k │ ├── contigs.bed │ ├── contigs.bed-1.svg │ ├── contigs.bed.svg │ ├── contigs.list │ ├── hifiasm.bed │ ├── otherLTR │ └── 01_run_draw.sh │ └── re_map_to_contigs │ ├── 01_run_get_mapped_bed.sh │ ├── 02_draw_read_depth.sh │ └── map ├── Step4_local_assembly ├── cal_otherLTR_length.sh └── check_read_repeat_length.pl ├── Step8_check_assembly_correctness ├── 01_run_get_mapped_bed.sh ├── 02_draw_read_depth.sh ├── 03_run_get_mapped_infor.sh ├── 04_draw_read_infor.sh ├── drawContigDepth.pl ├── drawReadsMap.pl ├── draw_mapping.pl ├── get_mapped_bed.pl ├── get_mapped_reads_infor.pl └── showReadsOnTheseRegion │ ├── 01_run_get_mapped_reads.sh │ ├── 02_get_region_read.sh │ ├── 03_get_read_list_and_extract_read.sh │ ├── 04_anno_reads.sh │ ├── 05_map_to_contig.sh │ ├── 06_prepare_draw_file.sh │ ├── 07_draw.sh │ ├── closed.bed │ ├── generate_mapping_files.pl │ ├── get_mapped_bed.pl │ ├── otherLTR │ ├── real4reads │ │ ├── 01_seqkit_bedtools.sh │ │ ├── 02_makeblastdb.sh │ │ ├── 03_self_blast.sh │ │ ├── 04_pairs_blast.sh │ │ ├── 05_extract_result.sh │ │ ├── drawTriangularCorr.pl │ │ └── run_draw.sh │ └── use_asm_to_check │ │ ├── ctg_graph000 │ │ └── 01_run_map.sh │ │ ├── ctg_graph070 │ │ └── 01_run_map.sh │ │ ├── ctg_graph085 │ │ └── 01_run_map.sh │ │ ├── local_asm_ont │ │ └── 01_run_map.sh │ │ └── local_asm_pb │ │ └── 01_run_map.sh │ ├── pacbio_region.bed │ ├── region.bed │ └── target.bed └── scripts ├── assembly ├── from_paf_get_the_mapping_position_of_scaffolds.pl └── orient_correct.pl ├── drawContigDepth.pl ├── drawContigRepeat.pl ├── drawRDNA.pl ├── drawRepeatInAnyRegion.pl ├── draw_mapping.pl ├── generate_shell.pl ├── map ├── convert_infor_to_linkview.pl ├── convert_paf_to_linkview.pl └── get_the_detailed_mapping_information_from_bwa_bam_file.pl └── read_extend_contig ├── change_pos_in_reverse.pl ├── choose_coverage_enough.pl ├── choose_span_enough.pl ├── concate_seq.py ├── drawContigRepeat.pl ├── extract_gap_500k_paf.pl ├── extract_mapped_reads.pl ├── extract_type.pl ├── linkview.pl ├── prepare_linkviewk.pl ├── show_routine_linkviewk.pl ├── span_enough_length.pl └── summarize_ssr_sequence.pl /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LAILAB-CAU/update-Mo17/HEAD/.gitattributes -------------------------------------------------------------------------------- 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