SPUMONI 2: improved classification using a pangenome index of minimizer digests.
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ABSTRACT:
SUBMITTER: Ahmed OY
PROVIDER: S-EPMC10197461 | biostudies-literature | 2023 May
REPOSITORIES: biostudies-literature
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SPUMONI 2: improved classification using a pangenome index of minimizer digests.
Ahmed Omar Y OY Rossi Massimiliano M Gagie Travis T Boucher Christina C Langmead Ben B
Genome biology 20230518 1
Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a novel sampled document array. By incorporating minimizers, SPUMONI 2's index is 65 times smaller than minimap2's for a mock community pangenome. SPUMONI 2 achieves a speed improvement of 3-fold compared to SPUMONI and 15-fold compared to minimap2. We show SPUMONI ...[more]
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