ArticleBioinformatics (Oxford, England)2023
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.Nature biotechnology · 2026Article
- k-mer-based approaches to unlock genebank genomics for targeted crop improvement.Nature genetics · 2026Review
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- Evaluation of high-throughput sequencing for replacing the conventional adventitious virus detection assays used for biologics.NPJ vaccines · 2025Article
- Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.Journal of translational medicine · 2025Article
- Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.Microbiome · 2025Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.PLoS computational biology · 2025Article
- Hybridization capture sequencing formBio · 2025Article
- StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.Bioinformatics (Oxford, England) · 2025Article
- Rapid species-level metagenome profiling and containment estimation with sylph.Nature biotechnology · 2025Article
- Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.NPJ biofilms and microbiomes · 2025Article
- Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.Bioinformatics (Oxford, England) · 2025Article
- Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology.Briefings in bioinformatics · 2025Article
- Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.mSystems · 2025Article
- Metagenomic estimation of dietary intake from human stool.Nature metabolism · 2025Article
- Article
- Metagenomic investigation of viruses in green sea turtles (Frontiers in microbiology · 2025Article
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8 authors.
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Abstract
motivationThe growing number of microbial reference genomes enables the improvement of metagenomic profiling accuracy but also imposes greater requirements on the indexing efficiency, database size and runtime of taxonomic profilers. Additionally, most profilers focus mainly on bacterial, archaeal and fungal populations, while less attention is paid to viral communities.
resultsWe present KMCP (K-mer-based Metagenomic Classification and Profiling), a novel k-mer-based metagenomic profiling tool that utilizes genome coverage information by splitting the reference genomes into chunks and stores k-mers in a modified and optimized Compact Bit-Sliced Signature Index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods. Benchmarking results based on simulated and real data demonstrate that KMCP, despite a longer running time than all other methods, not only allows the accurate taxonomic profiling of prokaryotic and viral populations but also provides more confident pathogen detection in clinical samples of low depth. AVAILABILITY AND IMPLEMENTATION: The software is open-source under the MIT license and available at https://github.com/shenwei356/kmcp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.