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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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T2T CHM13 human reference genome #3612

Open mjsteinbaugh opened 2 years ago

mjsteinbaugh commented 2 years ago

The Telomere-to-Telomere (T2T) consortium has released a full build of the human genome based on the CHM13hTERT cell line, described here: https://github.com/marbl/CHM13

The complete genome is available on NCBI here: https://www.ncbi.nlm.nih.gov/assembly/GCA_009914755.3

I'm interested in testing this out compared to GRCh38/hg38, and was wondering if we can add this as a pre-built default genome for bcbio alongside hg38.

T2T website is here, for reference: https://sites.google.com/ucsc.edu/t2tworkinggroup

naumenko-sa commented 2 years ago

yes, this is a big update. ok, let us do it!

amizeranschi commented 2 years ago

Hello, is there any progress into adding CHM13 as a default bcbio genome?

mjsteinbaugh commented 2 years ago

I'll look into building indices of this genome against salmon, kallisto, HISAT2, STAR, and RSEM.

mjsteinbaugh commented 2 years ago

Special issue on T2T is out today in Science: https://www.science.org/toc/science/376/6588

amizeranschi commented 2 years ago

Great stuff, many thanks for the link!