CoverM: read alignment statistics for metagenomics

• DOI: 10.1093/bioinformatics/btaf147
• Publication Date: 2025-04-08T02:34:03Z
• Authors: Samuel T N Aroney; Rhys J P Newell; Jakob N Nissen; Antonio Pedro Cam...; Gene W Tyson; Ben J Woodcroft
• Keywords: Python

Abstract Summary Genome-centric analysis of metagenomic samples is a powerful method for understanding the function microbial communities. Calculating read coverage central part analysis, enabling differential binning recovery genomes and estimation community composition. Coverage determined by processing alignments to reference sequences either contigs or genomes. Per-reference typically calculated in an ad-hoc manner, with each software package providing its own implementation specific definition coverage. Here we present unified CoverM which calculates several statistics ergonomic flexible manner. It uses ‘Mosdepth arrays’ computational efficiency avoids unnecessary I/O overhead calculating from streamed alignment results. Availability Implementation free available at https://github.com/wwood/coverm. implemented Rust, Python (https://github.com/apcamargo/pycoverm) Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.