ArticleBioinformatics (Oxford, England)2025
CoverM: read alignment statistics for metagenomics.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 297 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
297 citing papers in PubMed.
- Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.Gut microbes · 2026Article
- Article
- Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.Gut microbes · 2026Article
- Decoding strain level interactions betweenVirulence · 2026Article
- Article
- Fish gut-water interface as a hotspot for the dissemination of antibiotic resistance genes across natural and aquaculture systems.Current research in microbial sciences · 2026Article
- Soil proteogenomics uncover microbial strategies for soil depth-specific carbon cycling under whole-soil warming conditions.Nature communications · 2026Article
- Sex- and Time-Resolved Physiological and Gut Ecosystem Responses to a Food-Grade Microbiome-Targeted Intervention in Collegiate Endurance Athletes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- High diversity but limited expression of biosynthetic gene clusters in a peatland microbial community.Nature communications · 2026Article
- In situ evidence of tiered adaptations buffering a chemosynthetic clam holobiont against environmental sulfide fluctuations.Science advances · 2026Article
- Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.Journal of advanced research · 2026Article
- Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.The Journal of investigative dermatology · 2026Article
- Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts.mSystems · 2026Article
- Distinct Evolutionary Selection Patterns in Temperate and Filamentous Phages of Phocaeicola vulgatus in Health and IBD.Research square · 2026Article
- Metagenome-assembled genomes of papillomaviruses from mallard and northern pintail cloacal swabs.Microbiology resource announcements · 2026Article
- Article
- New Parvovirus and Other Swab-Associated Viruses Identified in the Eurasian Goshawk (Pathogens (Basel, Switzerland) · 2026Article
- Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome.Genome biology and evolution · 2026Article
- Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.Journal of animal science and biotechnology · 2026Article
237 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
summaryGenome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results. AVAILABILITY AND IMPLEMENTATION: CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.