{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Ahmed OY"],"funding":["Natural Sciences and Engineering Research Council of Canada","Office of Advanced Cyberinfrastructure","Division of Biological Infrastructure","NHGRI NIH HHS","National Human Genome Research Institute"],"pagination":["122"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10197461"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["24(1)"],"pubmed_abstract":["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."],"journal":["Genome biology"],"pubmed_title":["SPUMONI 2: improved classification using a pangenome index of minimizer digests."],"pmcid":["PMC10197461"],"funding_grant_id":["1920103","DBI-2029552","RGPIN-07185-2020","R01HG011392"],"pubmed_authors":["Gagie T","Langmead B","Ahmed OY","Boucher C","Rossi M"],"additional_accession":[]},"is_claimable":false,"name":"SPUMONI 2: improved classification using a pangenome index of minimizer digests.","description":"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.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 May","modification":"2024-11-13T16:51:32.52Z","creation":"2024-11-13T16:51:32.52Z"},"accession":"S-EPMC10197461","cross_references":{"pubmed":["37202771"],"doi":["10.1186/s13059-023-02958-1"]}}