CoverM aims to be a configurable, easy to use and fast read coverage calculator focused on metagenomics applications.
Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference FASTA sequences.
CoverM calculates the coverage either or genomes/MAGs (coverm genome) or individual contigs (coverm contig).
To install CoverM, the most straightforward way is to download the statically compiled binaries available on the releases page.
CoverM can also be installed from source, using the cargo build system after installing Rust. CoverM is not currently on crates.io.
For the full suite of options, these additional programs must be installed:
``` Main modes: contig Calculate coverage of contigs genome Calculate coverage of genomes
Utilities: make Generate BAM files through alignment filter Remove alignments with insufficient identity
Other options: -V, --version Print version information ```
For detailed usage see coverm <command> -h.
CoverM is made available under GPL3+. See LICENSE.txt for details. Copyright Ben Woodcroft.
Developed by Ben Woodcroft at the Australian Centre for Ecogenomics.