This is the track hub directory for the T2T CHM13 v2.0 assembly of the UCSC Genome Browser (the internal assembly name is "hs1", but we suggest using CHM13 in publications). This directory contains the genome sequence and all annotations as files in "UCSC Track Hub" format. This is different from other human genome assemblies such as hg38 which we used to keep in MySQL databases to some extent. The CHM13 genome browser is entirely built from binary indexed files, all referenced from a single hub.txt file that defines the annotation tracks. A full description of the file formats is here: https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html The hub.txt file that defines the track names and pointers to the data file is here: https://hgdownload.soe.ucsc.edu/gbdb/hs1/hubs/public/hub.txt It points to this genome sequence file in twoBit format: https://hgdownload.soe.ucsc.edu/gbdb/hs1/hs1.2bit If you are looking for ASCII text file, e.g. FASTA for the assembly or GFF with the gene models, of liftOver chain files, these are here: https://hgdownload.soe.ucsc.edu/goldenPath/hs1 The bigZips/ subdirectory there contains the assembly and gene models.
Name Last modified Size Description
Parent Directory - bbi/ 2022-09-21 08:56 - catLiftOffGenesV1/ 2022-09-21 08:56 - censat/ 2022-09-21 08:56 - chainNet/ 2024-08-02 19:19 - clinVar20220313/ 2022-09-21 08:56 - crispr/ 2024-01-30 16:26 - cytoBandMapped/ 2022-09-21 08:56 - dbSNP155/ 2022-09-21 09:02 - encode/ 2022-09-21 09:14 - gwasSNPs2022-03-08/ 2022-09-21 09:15 - hgCactus/ 2022-09-21 09:15 - hgLiftOver/ 2022-09-21 09:15 - hgUnique/ 2022-09-21 09:15 - hoffmanMappability/ 2023-11-30 09:50 - hs1.2bit 2022-07-16 14:27 775M html/ 2024-12-04 13:44 - hubs/ 2024-11-04 12:12 - ixIxx/ 2022-09-21 09:15 - liftOver/ 2023-06-13 16:10 - microsatellites/ 2022-09-21 09:15 - ncbiRefSeq/ 2023-05-29 11:06 - problematic/ 2024-11-03 18:54 - proseq/ 2023-08-15 16:41 - rdnaModel/ 2022-09-21 09:16 - rnaseq/ 2022-09-21 09:16 - sedefSegDups/ 2022-09-21 09:16 - sgdpCopyNumber/ 2022-09-21 09:20 - t2tRepeatMasker/ 2022-09-21 09:20 - trackDb.ix 2024-12-04 11:05 533K trackDb.ixx 2024-12-04 11:05 144 trackDb.offsets 2024-12-04 11:05 26K trackDb.offsets.ixx 2024-12-04 11:05 26 trackDb.txt 2024-12-04 11:05 215K