Journal ArticleSPUMONI 2: improved classification using a pangenome index of minimizer digestsAhmed, Omar Y.; Rossi, Massimiliano; Gagie, Travis; Boucher, Christina; Langmead, BenAbstract 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 2 achieves an advantageous mix of accuracy and efficiency in practical scenarios such as adaptive sampling, contamination detection and multi-class metagenomics classification.2023-12-0110451197Genome Biology2411474-760Xhttps://doi.org/10.1186/s13059-023-02958-12029552; 2013998National Science Foundation