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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(!)
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
Concretely, we associate to each <partition/fingerprint_value>pair the list of genomes that got this fingerprint value in this partition.
This means that a query will only generate one costly "Random Access" per partition.
This means that a query will only generate one costly "Random Access" per partition.
