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

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

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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  • McIntyre, Alexa B. R., Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, et al. 2017. “Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers.” Genome Biology 18: 182. https://dx.doi.org/10.1186/s13059-017-1299-7
  • Ondov, Brian D., Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren, and Adam M. Phillippy. 2016. “Mash: Fast Genome and Metagenome Distance Estimation Using MinHash.” Genome Biology 17: 132. https://dx.doi.org/10.1186/s13059-016-0997-x
  • Solomon, Brad, and Carl Kingsford. 2016. “Fast Search of Thousands of Short-Read Sequencing Experiments.” Nature Biotechnology 34 (3): 300–302. https://dx.doi.org/10.1038/nbt.3442
  • Titus Brown, C., and Luiz Irber. 2016. “sourmash: A Library for MinHash Sketching of DNA.” The Journal of Open Source Software 1 (5). https://dx.doi.org/10.21105/joss.00027
  • Wood, Derrick E., and Steven L. Salzberg. 2014. “Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments.” Genome Biology 15 (3): R46. https://dx.doi.org/10.1186/gb-2014-15-3-r46