ArticleNucleic acids research2017
k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.Briefings in bioinformatics · 2024Article
- A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.eLife · 2024Article
- Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.Genome biology and evolution · 2024Article
- Comparative analysis of metagenomic classifiers for long-read sequencing datasets.BMC bioinformatics · 2024Article
- Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice.Genes · 2022Article
- Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic.Scientific reports · 2022Article
- Evaluation of Urethrotropic-Clade Meningococcal Infection by Urine Metagenomic Shotgun Sequencing.Journal of clinical microbiology · 2022Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Associations between stool micro-transcriptome, gut microbiota, and infant growth.Journal of developmental origins of health and disease · 2021Article
- Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs.mSphere · 2021Article
- A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.Computational and structural biotechnology journal · 2021Review
- Full Molecular Typing of Neisseria meningitidis Directly from Clinical Specimens for Outbreak Investigation.Journal of clinical microbiology · 2020Article
- IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.GigaScience · 2020Article
- The use of taxon-specific reference databases compromises metagenomic classification.BMC genomics · 2020Article
- Review
- A review of methods and databases for metagenomic classification and assembly.Briefings in bioinformatics · 2019Review
- gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.Nucleic acids research · 2019Article
- An Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis.Frontiers in genetics · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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.
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Registered trials
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