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dib-lab / distillerycats

Find disease associations across metagenomes with k-mers using sourmash, and then recover pangenomic accessory elements using spacegraphcats.
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Bifrost #9

Open nmb85 opened 3 years ago

nmb85 commented 3 years ago

Would the Bifrost (I believe it is actually pronounced very similarly to beef roast) colored deBruijn graph structure provide any utility here? Applying spacegraphcats to colored cDBGs is one of the things you suggested, I believe: "Potential applications of spacegraphcats in metagenomics include developing metrics for genome binning quality, analyzing pangenome neighborhood structure, exploring r-dominating sets for r>1, extending analyses to colored De Bruijn graphs, and investigating de novo extraction of genomes based on neighborhood content."

Separately, I believe distillery cats would love beef roast.

A BLAST-like application recently built atop Bifrost

A component used in Pyseer (bacterial GWAS) built atop Bifrost: https://github.com/johnlees/unitig-caller

taylorreiter commented 3 years ago

Hi @nmb85! The distillerycats pipeline wraps sourmash and spacegraphcats. It uses spacegraphcats to build and query cDBGs. spacegraphcats could certainly use take advantage of bifrost! See https://github.com/spacegraphcats/spacegraphcats/issues/297 and https://github.com/spacegraphcats/spacegraphcats/issues/308.

Thank you for including links to blastfrost and the GWAS application! I hadn't seen these applications before