CNRS researcher in the Bonsai team in the CRIStaL lab.
Work on genome assembly, read correction, graph alignment and data structures
Nov 5, 2021 • 11 tweets • 3 min read
So excited to share our latest preprint!
TLDR:
We present NIQKI, a Mash-like tool able to index large sequence databases.
Its main feature is to be fast!
We were able to index all bacterial genomes of GenBank (>1million) and query all pairwise distances in a couple of days(!)
Behind the scenes, we rely on a novel index structure to query partition-based fingerprints that we call NIQKI (Next Index to Query Kmer Intersection) which use an inverted index for each partition
