Add human reference genome to prepared databases

[dportik]

Hi Titus et al,
Given the recent fiasco related to mapping reads to microbial databases without human references (links at bottom), it might be a good time to create a small human genome database for use with sourmash. A standalone database on the database page would be ideal, so that researchers can include with the other databases of interest.

Thanks for considering!

social media discussion: https://twitter.com/StevenSalzberg1/status/1686350449069244416
pre-print: https://doi.org/10.1101/2023.07.28.550993

[luizirber]

On the "raw" side ¹ there are both GRCh38.p14 and T2T-CHM13v2.0 signatures in wort, would that work?

Footnotes

1. just downloaded the data and calculated a signature, no other pre-processing like repeat masking ↩

[dportik]

Yep! Those should be plenty.

[ctb]

Repo to sketch hg38, including all unmapped chromosomes: https://github.com/ctb/2024-human-sketch

[ctb]

note: decontaminating human WGS samples, #3151

[ctb]

download at: https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/hg38/hg38-entire.sig.zip