├── .gitignore ├── README.md ├── T2T_GenArk ├── README.md ├── T2T-CHM13v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── gen.trackDb.txt │ ├── grc.trackDb.txt │ ├── groups.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── genomes.txt ├── groups.txt ├── hal.trackDb.txt ├── html │ ├── aSatSF.html │ ├── aSatStrand.html │ ├── accessibilityMask.html │ ├── catGene.html │ ├── cenp-a.html │ ├── cenp-b_sites.html │ ├── censat.html │ ├── consGene.html │ ├── cpgMethyl.html │ ├── epi5mC.html │ ├── epigenetics.html │ ├── gc5Base.html │ ├── genomeFeature.html │ ├── isoseq.html │ ├── mhcGene.html │ ├── microsatellites.html │ ├── nonB.html │ ├── numt.html │ ├── phast.html │ ├── readCoverage.html │ ├── refGene.html │ ├── repliseq.html │ ├── rmsk.html │ ├── segDups.html │ ├── seqIdy.html │ ├── template.html │ ├── toga.html │ └── variant.html ├── hub.txt ├── mGorGor1_v2.0 │ ├── asm.trackDb.txt │ ├── cactus.trackDb.txt │ ├── com.trackDb.txt │ ├── gen.trackDb.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPanPan1_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── gen.trackDb.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPanTro3_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── gen.trackDb.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPonAbe1_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── gen.trackDb.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPonPyg2_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── gen.trackDb.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mSymSyn1_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── gen.trackDb.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ └── trackDb.txt └── maf.trackDb.txt ├── T2Tgenomes ├── HG002v1.0.1.MAT │ ├── chains.trackDb.txt │ ├── genark.trackDb.txt │ ├── rm.trackDb.txt │ └── trackDb.txt ├── HG002v1.0.1.PAT │ ├── chains.trackDb.txt │ ├── genark.trackDb.txt │ ├── rm.trackDb.txt │ └── trackDb.txt ├── HG002v1.0.1 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── fiberseq.trackDb.txt │ ├── html │ │ ├── GCA_018852605.2_ASM1885260v2.description.html │ │ ├── GCA_018852615.2_ASM1885261v2.description.html │ │ ├── SD_track.hg002v1.0.1.010624.html │ │ ├── curGen_track.html │ │ ├── errorKmerDescription.html │ │ ├── hetsitesDescription.html │ │ ├── nucfreqdescription.html │ │ └── rmsk.html │ ├── methyl.trackDb.txt │ ├── rep.trackDb.txt │ └── var.trackDb.txt ├── HG002v1.1.MAT │ ├── asm.trackDb.txt │ ├── chains.trackDb.txt │ ├── genes.trackDb.txt │ ├── rm.trackDb.txt │ ├── telo.trackDb.txt │ └── trackDb.txt ├── HG002v1.1.PAT │ ├── asm.trackDb.txt │ ├── chains.trackDb.txt │ ├── genes.trackDb.txt │ ├── rm.trackDb.txt │ ├── telo.trackDb.txt │ └── trackDb.txt ├── HG002v1.1 │ ├── com.trackDb.txt │ ├── fiberseq.trackDb.txt │ ├── hg002v1.1.chrom.sizes │ ├── html │ │ ├── CpGislandDescription.html │ │ ├── HG002v1.1.description.html │ │ ├── JHU_Liftoff.html │ │ ├── SD_track.hg002v1.1.013025.html │ │ ├── SPRQElementErrorKmerDescription.html │ │ ├── errorKmerDescription.html │ │ ├── hetsitesDescription.html │ │ ├── hg002v1.1.issues.html │ │ ├── hg002v1.1.issues.v4.html │ │ ├── hg002v1.1_to_ref_chains.description.html │ │ └── nucfreqdescription.html │ ├── methyl.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ └── var.trackDb.txt ├── KOLF2.1Jv1.1 │ ├── KOLF2.1Jv1.1_dip_noY.description.html │ ├── align.trackDb.txt │ ├── chain.trackDb.txt │ ├── gene.trackDb.txt │ ├── genomes.txt │ ├── groups.txt │ ├── hub.txt │ ├── met.trackDb.txt │ ├── trackDb.txt │ ├── trans.trackDb.txt │ └── var.trackDb.txt ├── T2T-CHM13v2.0 │ ├── asm.trackDb.txt │ ├── chm13v2.0.alias │ ├── chm13v2.0.sizes │ ├── com.trackDb.txt │ ├── cytoBand.as │ ├── cytoBand.bb │ ├── description.html │ ├── gen.trackDb.txt │ ├── grc.trackDb.txt │ ├── groups.txt │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── genomes.txt ├── groups.txt ├── hal.trackDb.txt ├── html │ ├── aSatSF.html │ ├── aSatStrand.html │ ├── accessibilityMask.html │ ├── catGene.html │ ├── cenp-a.html │ ├── cenp-b_sites.html │ ├── censat.html │ ├── consGene.html │ ├── cpgMethyl.html │ ├── epi5mC.html │ ├── epigenetics.html │ ├── gc5Base.html │ ├── genomeFeature.html │ ├── isoseq.html │ ├── mhcGene.html │ ├── microsatellites.html │ ├── nonB.html │ ├── numt.html │ ├── phast.html │ ├── readCoverage.html │ ├── refGene.html │ ├── repliseq.html │ ├── rmsk.html │ ├── segDups.html │ ├── seqIdy.html │ ├── template.html │ ├── toga.html │ └── variant.html ├── hub.txt ├── mGorGor1_v2.0 │ ├── asm.trackDb.txt │ ├── cactus.trackDb.txt │ ├── com.trackDb.txt │ ├── description.html │ ├── gen.trackDb.txt │ ├── mGorGor1_v2.0.alias │ ├── mGorGor1_v2.0.sizes │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mGorGor1_v2.0_pri │ ├── description.html │ └── mGorGor1_v2.0_pri.sizes ├── mPanPan1_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── description.html │ ├── gen.trackDb.txt │ ├── mPanPan1_v2.0.alias │ ├── mPanPan1_v2.0.sizes │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPanPan1_v2.0_pri │ ├── description.html │ └── mPanPan1_v2.0_pri.sizes ├── mPanTro3_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── description.html │ ├── gen.trackDb.txt │ ├── mPanTro3_v2.0.alias │ ├── mPanTro3_v2.0.chr.sizes │ ├── mPanTro3_v2.0.ideogram.bb │ ├── mPanTro3_v2.0.sizes │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPanTro3_v2.0_pri │ ├── description.html │ └── mPanTro3_v2.0_pri.sizes ├── mPonAbe1_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── description.html │ ├── gen.trackDb.txt │ ├── mPonAbe1_v2.0.alias │ ├── mPonAbe1_v2.0.sizes │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPonAbe1_v2.0_pri │ ├── description.html │ └── mPonAbe1_v2.0_pri.sizes ├── mPonPyg2_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── description.html │ ├── gen.trackDb.txt │ ├── mPonPyg2_v2.0.alias │ ├── mPonPyg2_v2.0.sizes │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ ├── trackDb.txt │ └── var.trackDb.txt ├── mPonPyg2_v2.0_pri │ ├── description.html │ └── mPonPyg2_v2.0_pri.sizes ├── mSymSyn1_v2.0 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── description.html │ ├── gen.trackDb.txt │ ├── mSymSyn1_v2.0.alias │ ├── mSymSyn1_v2.0.sizes │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ └── trackDb.txt ├── mSymSyn1_v2.0_pri │ ├── description.html │ └── mSymSyn1_v2.0_pri.sizes ├── mSymSyn1_v2.1 │ ├── asm.trackDb.txt │ ├── com.trackDb.txt │ ├── description.html │ ├── gen.trackDb.txt │ ├── mSymSyn1_v2.1.alias │ ├── mSymSyn1_v2.1.sizes │ ├── reg.trackDb.txt │ ├── rep.trackDb.txt │ ├── rna.trackDb.txt │ └── trackDb.txt └── maf.trackDb.txt ├── chain ├── mGorGor1_XY_v1.1_to_v2.0.chain ├── mGorGor1_XY_v2.0_to_v1.1.chain ├── mPanPan1_XY_v1.1_to_v2.0.chain ├── mPanPan1_XY_v2.0_to_v1.1.chain ├── mPanTro3_XY_v1.1_to_v2.0.chain ├── mPanTro3_XY_v2.0_to_v1.1.chain ├── mPonAbe1_XY_v1.1_to_v2.0.chain ├── mPonAbe1_XY_v2.0_to_v1.1.chain ├── mPonPyg2_XY_v1.1_to_v2.0.chain ├── mPonPyg2_XY_v2.0_to_v1.1.chain ├── mSymSyn1_XY_v1.1_to_v2.0.chain ├── mSymSyn1_XY_v2.0_to_v1.1.chain └── mSymSyn1_v2.1_to_v2.0.txt ├── html └── chm13 │ ├── accessibilityMask.html │ ├── censat.html │ ├── curGene.html │ ├── encode.html │ ├── epigenetics.html │ ├── fire.html │ ├── genomeFeature.html │ ├── haqer.html │ ├── isoseq.html │ ├── mappability.html │ ├── microsatellites.html │ ├── min_unique_kmer.html │ ├── phr.html │ ├── readCoverage.html │ ├── refGene.html │ ├── rmsk.html │ ├── sedefSegDups.html │ ├── segDups.html │ ├── sync.sh │ ├── unique_21_51_mer.html │ ├── v1_nflo_description.html │ └── validation.html ├── igv_session ├── README.md ├── chm13v2.0.json ├── chm13v2.0_alias.tab ├── chm13v2.0_cytobands_allchrs.txt ├── mPanPan1_v2.0.alias.txt ├── mPanPan1_v2.0.ideogram.bed ├── mPanPan1_v2.0.json ├── mPanTro3_v2.0.alias.txt ├── mPanTro3_v2.0.ideogram.bed ├── mPanTro3_v2.0.json └── rename.map ├── misc ├── README.md ├── bigChain.as ├── bigGenePred.as ├── bigLink.as ├── bigRmskAlignBed.as ├── bigRmskBed.as └── cytoBand.as └── src ├── CatRefConsensus └── README.md ├── CenSat ├── color_replace_chm13.txt ├── fix_rDNA_gap.py ├── recolor.map ├── to_bb.sh └── to_bb_chm13.sh ├── Centromere └── README.md ├── GeneAnnotation ├── README.md ├── gff3ToExtra.py ├── gff3ToGenePred ├── gff_to_bb.sh └── ixIxx ├── IsoSeq └── README.md ├── MHC ├── README.md ├── colors.txt ├── mGorGor1_MHC_manual_v0.1.bed ├── mGorGor1_MHC_manual_v0.1.txt ├── mPanPan1_MHC_manual_v0.1.bed ├── mPanPan1_MHC_manual_v0.1.txt ├── mPanTro3_MHC_manual_v0.1.bed ├── mPanTro3_MHC_manual_v0.1.txt ├── mPonAbe1_MHC_manual_v0.1.bed ├── mPonAbe1_MHC_manual_v0.1.txt ├── mPonPyg2_MHC_manual_v0.1.bed ├── mPonPyg2_MHC_manual_v0.1.txt ├── mSymSyn1_MHC_manual_v0.1.bed └── mSymSyn1_MHC_manual_v0.1.txt ├── NUMT └── README.md ├── RepeatMasker └── convert_upload.sh ├── RepliSeq └── README.md ├── SD └── README.md ├── TOGA └── README.md ├── bedToSparseWig.jar ├── chain_to_bigChain_GRCh_to_CHM13.sh ├── epi └── README.md ├── issues └── README.md ├── mSymSyn1_v2.0_v2.1.map ├── nonB_DNA └── README.md ├── path.txt ├── phast ├── README.md ├── approach_1.sh ├── approach_2.sh └── wig_to_bigWig.sh ├── primates.sh ├── seqIdy ├── README.md └── convert_tracks.sh ├── txtContains.jar ├── txtReplaceWords.jar ├── update_mSymSyn1_tracks.sh ├── variants └── README.md └── wfmash_chain ├── README.md ├── 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