CoverM: read alignment statistics for metagenomics

Journal Article · Sat Mar 29 00:00:00 EDT 2025 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btaf147· OSTI ID:2570293

Aroney, Samuel T N; Newell, Rhys J P; Nissen, Jakob N; Camargo, Antonio Pedro; Tyson, Gene W; Woodcroft, Ben J

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/CoverM_jll.jl) interfaces.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: US Department of Energy; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Biological Systems Science Division (SC-23.2 )
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 2570293
• Journal Information: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 4 Vol. 41
• Country of Publication: United States
• Language: English