├── .DS_Store ├── .gitignore ├── Genome_synteny ├── README.md ├── bin │ ├── artificial_chrs_for_synteny.py │ ├── comparison_synteny.py │ ├── filter_blocks_by_ratio.py │ ├── preCircosLink.py │ ├── preCircosLink.sort.py │ ├── split_blocks_by_Chrs.py │ └── synteny_stat.py └── example │ ├── all.lens │ ├── artificial_chrs.png │ ├── circos.conf │ ├── circos.svg │ ├── karyotype.txt │ ├── link.txt │ ├── linkbyChrs │ ├── PEQU01000001.1 │ │ ├── PEQU01000001.1.txt │ │ ├── karyotype.txt │ │ ├── link.txt │ │ └── single_chr.png │ ├── PEQU01000002.1 │ │ └── PEQU01000002.1.txt │ ├── PEQU01000003.1 │ │ └── PEQU01000003.1.txt │ ├── PEQU01000004.1 │ │ └── PEQU01000004.1.txt │ ├── PEQU01000005.1 │ │ └── PEQU01000005.1.txt │ ├── PEQU01000006.1 │ │ └── PEQU01000006.1.txt │ ├── PEQU01000007.1 │ │ └── PEQU01000007.1.txt │ ├── PEQU01000008.1 │ │ └── PEQU01000008.1.txt │ ├── PEQU01000009.1 │ │ └── PEQU01000009.1.txt │ ├── PEQU01000010.1 │ │ └── PEQU01000010.1.txt │ ├── PEQU01000011.1 │ │ └── PEQU01000011.1.txt │ ├── PEQU01000012.1 │ │ └── PEQU01000012.1.txt │ ├── PEQU01000013.1 │ │ └── PEQU01000013.1.txt │ ├── PEQU01000014.1 │ │ └── PEQU01000014.1.txt │ ├── PEQU01000015.1 │ │ └── PEQU01000015.1.txt │ └── PEQU01000016.1 │ │ └── PEQU01000016.1.txt │ ├── pair_chrs.png │ ├── pair_chrs.sort.png │ ├── querry.lens │ ├── ref.lens │ └── test.link ├── Python_plot ├── 96well_md.py ├── Matplotlib.pdf ├── density.py ├── lifecycle.py ├── sales.ai ├── sales.pdf ├── sales.png ├── samples.assignment.sorted.log ├── test.data ├── test_bar1.py └── test_bar2.py ├── README.md ├── Trees ├── README.md └── make_colorConfig_for_nwk.py ├── alignment ├── depth_plotter.py └── muscle2link │ ├── link_muscle.pl │ └── link_muscle.py ├── asm2ref ├── .DS_Store ├── blast │ ├── preCircosLink.sort.py │ └── run_blast_links.sh ├── mashmap │ └── run_unimap_dotplot.sh ├── mummer │ ├── confs │ │ ├── run_asm2ref_mummer_highlights.conf │ │ └── run_asm2ref_mummer_links.conf │ ├── mummer4 │ ├── preCircosHighlight.sort.py │ ├── preCircosLink.sort.py │ ├── run_asm2ref_mummer_highlights.sh │ └── run_asm2ref_mummer_links.sh ├── preCircosLink.sort.py ├── unimap_minimap │ ├── README.md │ ├── confs │ │ └── circos.conf │ ├── generateDotPlot │ ├── ggplot2_paf.r │ ├── merge_region.py │ ├── preCircosLinkFromPaf.sort.py │ ├── run_asm2ref_paf2links.sh │ ├── run_paf2dotplot.sh │ ├── split_alignment_by_Chrs.py │ └── unimap └── visualize_tools │ ├── LINKVIEW.py │ └── generateDotPlot ├── assembly ├── README.md └── pair_end_in_scaffold.pl ├── common_bin └── generate_cols.py ├── dotplot ├── DotPlot │ ├── SVG │ │ └── SVGLAB.pm │ └── bin │ │ └── Draw_Dot.pl └── readme.md └── mito2circos ├── .DS_Store ├── CHANGE.log ├── README.md ├── auto_depth ├── .DS_Store ├── circos.depth.txt ├── draw_circos_for_mitogenome_auto_depth.pl ├── example │ ├── circos.bam │ ├── circos.conf │ ├── circos.dep │ ├── circos.depth.txt │ ├── circos.fa.gc.txt │ ├── circos.features.txt │ ├── circos.gene.text.txt │ ├── circos.karyotype.txt │ ├── circos.map.sh │ ├── circos.mito.fa │ ├── circos.png │ ├── circos.sorted.bam │ ├── circos.strand.text.txt │ └── circos.svg ├── mitogenome.auto_depth.conf ├── random_depth.py └── work.sh ├── data ├── SRR7174336.mitoscaf.fa.gbf ├── SRR7174336_1.demo.fq.gz └── SRR7174336_2.demo.fq.gz ├── map2mitoCircos ├── .DS_Store ├── README.md ├── circos.conf ├── depth.txt ├── karyotype.txt ├── map2mitoCircos.conf ├── map_mito_depth.py ├── map_mito_depth.v1.py ├── outdir │ ├── circos.conf │ ├── circos.png │ ├── depth.txt │ ├── feature.txt │ └── karyotype.txt └── references.fa ├── multi-circos_in_oneimage ├── draw_multi-circos_in_oneimage.conf ├── draw_multi-circos_in_oneimage.pl ├── draw_multi-circos_in_oneimage_byclass.conf └── draw_multi-circos_in_oneimage_byclass.pl └── standard ├── .DS_Store ├── draw_circos_for_mitogenome_standard.pl ├── example ├── NC_031379.circos.conf ├── NC_031379.fa.gc.txt ├── NC_031379.features.txt ├── NC_031379.gene.text.txt ├── NC_031379.karyotype.txt ├── NC_031379.png ├── 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