CoverM: read alignment statistics for metagenomics
2025/01/20 by Samuel T. N. Aroney, Rhys J. P. Newell, R.B. Newell +7 · 1 voice · 432 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · Mathematics · #Biology #Computational biology #Computer science #Genetics #Genomics and Phylogenetic Studies #Gut microbiota and health #Mathematics #Metagenomics #Microbial Community Ecology and Physiology #Statistics
paper · pdf · doi:10.1093/bioinformatics/btaf147
published in Bioinformatics 41(4) (Oxford University Press)
openalex publication_date 2025/03/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
Abstract
SUMMARY: Genome-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/CoverMjll.jl) interfaces.
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