Josh Millwood
@jmillwood.bsky.social
820 followers
2.6K following
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Husband | Furdad | Professional eater | Asst. professor, Univ. of West Alabama | PhD candidate, Univ. of Alabama (ABD) | Ecological Genomics | Aquatic Inverts | Lover of AL and the Good South | Roll Tide! | Go Tigers! | he/him 🏳️🌈🏳️⚧️✊🏿Ally | Opinions are mine
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Josh Millwood
@jmillwood.bsky.social
· Jan 18
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Titus Brown
@titus.idyll.org
· 17h
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2 - Genome Biology
The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck. We present Cuttlefish 2, significantly advancing the state-of-the-art for this problem. On a commodity server, it reduces the graph construction time for 661K bacterial genomes, of size 2.58Tbp, from 4.5 days to 17–23 h; and it constructs the graph for 1.52Tbp white spruce reads in approximately 10 h, while the closest competitor requires 54–58 h, using considerably more memory.
genomebiology.biomedcentral.com
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood
Reposted by Josh Millwood