coverm

Read coverage calculator for metagenomics

CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. CoverM calculates coverage of genomes/MAGs `coverm genome` or individual contigs `coverm contig`. Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in various formats.