luizirber / 2018-sms

Poster and talk presented at Bioinformatics for the Microbiome Symposium at Stanford on 2018-09-24

A new method for taxonomic classification using MinHash and Sequence Bloom Trees

• Luiz Carlos Irber Júnior

• Philip Brooks

• Taylor Reiter

• C. Titus Brown

• Department of Population Health and Reproduction, University of California, Davis, USA

Poster and talk presented at Bioinformatics for the Microbiome Symposium at Stanford on 2018-09-24.

Abstract

We introduce sourmash gather, a new method for taxonomic classification using MinHash and Sequence Bloom Trees. We ran the NIST-IMMSA benchmark and gather has better precision and recall than other tools.

gather uses the same Sequence Bloom Tree index we already use for searching similar datasets in public databases (like RefSeq and GenBank), but a different search strategy: instead of looking for all datasets above a similarity threshold, gather does a greedy search for the best match, report it and then remove the match from the query. This process is repeated while there are enough items in the query to find matches above a certain threshold.

gather is a new feature in sourmash 2.0, available on Bioconda and PyPI.

References

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