title: k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets.
abstract: k-SLAM is a highly efficient algorithm for the characterization of metagenomic data. Unlike other ultra-fast metagenomic classifiers, full sequence alignment is performed allowing for gene identification and variant calling in addition to accurate taxonomic classification. A k-mer based method provides greater taxonomic accuracy than other classifiers and a three orders of magnitude speed increase over alignment based approaches. The use of alignments to find variants and genes along with their taxonomic origins enables novel strains to be characterized. k-SLAM's speed allows a full taxonomic classification and gene identification to be tractable on modern large data sets. A pseudo-assembly method is used to increase classification accuracy by up to 40% for species which have high sequence homology within their genus.
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, SW7 2AZ, London, UK.
authors.forename: David
authors.initials: D
authors.lastname: Ainsworth
authors.affiliation: Centre for Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, SW7 2AZ, London, UK.
authors.forename: Michael J E
authors.initials: MJE
authors.lastname: Sternberg
authors.affiliation: Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
authors.forename: Come
authors.initials: C
authors.lastname: Raczy
authors.affiliation: Bioinformatics Data Science Group, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ, London, UK.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Butcher
mesh_terms: D000465:Algorithms; D016022:Case-Control Studies; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D058893:DNA Barcoding, Taxonomic / Q000379:methods* / Q000592:standards; D000069196:Gastrointestinal Microbiome; D016680:Genome, Bacterial; D006801:Humans; D008103:Liver Cirrhosis / Q000382:microbiology; D054892:Metagenome; D056186:Metagenomics / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D054323:Shiga-Toxigenic Escherichia coli / Q000145:classification / Q000235:genetics