A new method for taxonomic classification using MinHash and Sequence Bloom Trees
Department of Population Health and Reproduction, University of California, Davis, USA
We introduce sourmash gather, a new method for taxonomic classification using
MinHash and Sequence Bloom Trees. We ran the NIST-IMMSA benchmark and
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
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.
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