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biocommons / uta

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
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Add support for the telomer-to-telomer assembly (T2T) #234

Open andreasprlic opened 3 years ago

andreasprlic commented 3 years ago

Recently a new assembly was published, which looks like a potential successor for GRCh38. It would be nice to get support for it in UTA. I guess we don't have it yet in RefSeq, but hopefully that will change soon. So far there's this .

davmlaw commented 1 year ago

I've added T2T in cdot, here's where I got the transcripts:

RefSeq transcripts:

https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2023_03/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz

Ensembl transcripts:

https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/geneset/2022_06/Homo_sapiens-GCA_009914755.4-2022_06-genes.gff3.gz https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/geneset/2022_07/Homo_sapiens-GCA_009914755.4-2022_07-genes.gff3.gz

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