CoverM
Overview
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.
Version 0.7.0 is installed on the CSF.
Restrictions on use
CoverM is made available under GPL3+.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load the following modulefile:
module load apps/binapps/coverm/0.7.0
Running the application
Please do not run CoverM on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Ensure that your input files are in the directory from which you wish to run your job.
Create a batch submission script (which will load the modulefile in the jobscript) in the same directory, for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory module load apps/binapps/coverm/0.7.0 coverm genome <GENOME_DESCRIPTION> <MAPPING_INPUT> ..
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Ensure that your input files are in the directory from which you wish to run your job.
Create a batch submission script (which will load the modulefile in the jobscript) in the same directory, for example:
#!/bin/bash --login #$ -cwd #$ -pe smp.pe 8 ## $NSLOTS below automatially sets to the number requested here module load apps/binapps/coverm/0.7.0 coverm genome -t $NSLOTS <GENOME_DESCRIPTION> <MAPPING_INPUT> ..
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Interactive use
Further info
Updates
None.