coverm
Link to section 'Introduction' of 'coverm' Introduction
Coverm is a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.
For more information, please check its website: https://biocontainers.pro/tools/coverm and its home page on Github.
Link to section 'Versions' of 'coverm' Versions
- 0.6.1
Link to section 'Commands' of 'coverm' Commands
- coverm
Link to section 'Module' of 'coverm' Module
You can load the modules by:
module load biocontainers
module load coverm
Link to section 'Example job' of 'coverm' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Coverm on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=coverm
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers coverm
coverm genome --genome-fasta-files xcc.fasta --coupled SRR11234553_1.fastq SRR11234553_2.fastq