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CoverM

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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 (help) or individual contigs coverm contig (help). Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in various formats.

Installation

Install through the bioconda package

CoverM and its dependencies can be installed through the bioconda conda channel. After initial setup of conda and the bioconda channel, it can be installed with

conda install coverm

Pre-compiled binary

Statically compiled CoverM binaries available on the releases page. This installation method requires non-Rust dependencies to be installed separately - see the dependencies section.

Compiling from source

CoverM can also be installed from source, using the cargo build system after installing Rust.

cargo install coverm

Development version

To run an unreleased version of CoverM, after installing Rust and any additional dependencies listed below:

git clone https://github.com/wwood/CoverM
cd CoverM
cargo run -- genome ...etc...

To run tests:

cargo build
cargo test

Dependencies

For the full suite of options, additional programs must also be installed, when installing from source or for development.

These can be installed using the conda YAML environment definition:

conda env create -n coverm -f coverm.yml

Or, these can be installed manually:

  • samtools v1.9
  • tee, which is installed by default on most Linux operating systems.
  • man, which is installed by default on most Linux operating systems.

and some mapping software:

For dereplication:

Shell completion

Completion scripts for various shells e.g. BASH can be generated. For example, to install the bash completion script system-wide (this requires root privileges):

coverm shell-completion --output-file coverm --shell bash
mv coverm /etc/bash_completion.d/

It can also be installed into a user's home directory (root privileges not required):

coverm shell-completion --shell bash --output-file /dev/stdout >>~/.bash_completion

In both cases, to take effect, the terminal will likely need to be restarted. To test, type coverm gen and it should complete after pressing the TAB key.

Usage

CoverM operates in several modes. Detailed usage information including examples is given at the links below, or alternatively by using the -h or --full-help flags for each mode:

  • genome - Calculate coverage of genomes
  • contig - Calculate coverage of contigs

There are several utility modes as well:

  • make - Generate BAM files through alignment
  • filter - Remove (or only keep) alignments with insufficient identity
  • cluster - Dereplicate and cluster genomes
  • shell-completion - Generate shell completion scripts

Calculation methods

The -m/--methods flag specifies the specific kind(s) of coverage that are to be calculated.

To illustrate, imagine a set of 3 pairs of reads, where only 1 aligns to a single reference contig of length 1000bp:

read1_forward    ========>
read1_reverse                                  <====+====
contig    ...-----------------------------------------------------....
                 |        |         |         |         |
position        200      210       220       230       240

The difference coverage measures would be:

Method Value Formula Explanation
mean 0.02235294 (10+9)/(1000-2*75) The two reads have 10 and 9 bases aligned exactly, averaged over 1000-2*75 bp (length of contig minus 75bp from each end).
relative_abundance 33.3% 0.02235294/0.02235294*(2/6) If the contig is considered a genome, then its mean coverage is 0.02235294. There is a total of 0.02235294 mean coverage across all genomes, and 2 out of 6 reads (1 out of 3 pairs) map. This coverage calculation is only available in 'genome' mode.
trimmed_mean 0 mean_coverage(mid-ranked-positions) After removing the 5% of bases with highest coverage and 5% of bases with lowest coverage, all remaining positions have coverage 0.
covered_fraction 0.02 (10+10)/1000 20 bases are covered by any read, out of 1000bp.
covered_bases 20 10+10 20 bases are covered.
variance 0.01961962 var({1;20},{0;980}) Variance is calculated as the sample variance.
length 1000 The contig's length is 1000bp.
count 2 2 reads are mapped.
reads_per_base 0.002 2/1000 2 reads are mapped over 1000bp.
metabat contigLen 1000, totalAvgDepth 0.02235294, bam depth 0.02235294, variance 0.01961962 Reproduction of the MetaBAT 'jgi_summarize_bam_contig_depths' tool output, producing identical output.
coverage_histogram 20 bases with coverage 1, 980 bases with coverage 0 The number of positions with each different coverage are tallied.
rpkm 1000000 2 * 10^9 / 1000 / 2 Calculation here assumes no other reads map to other contigs. See https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ for an explanation of RPKM and TPM
tpm 1000000 rpkm/total_of_rpkm * 10^6 Calculation here assumes no other reads map to other contigs. See RPKM above.

Calculation of genome-wise coverage (genome mode) is similar to calculating contig-wise (contig mode) coverage, except that the unit of reporting is per-genome rather than per-contig. For calculation methods which exclude base positions based on their coverage, all positions from all contigs are considered together. For instance, if a 2000bp contig with all positions having 1X coverage is in a genome with 2,000,000bp contig with no reads mapped, then the trimmed_mean will be 0 as all positions in the 2000bp are in the top 5% of positions sorted by coverage.

License

CoverM is made available under GPL3+. See LICENSE.txt for details. Copyright Ben Woodcroft.

Developed by Ben Woodcroft at the Queensland University of Technology Microbiome Research Group.