metabat
Link to section 'Introduction' of 'metabat' Introduction
Metabat is a robust statistical framework for reconstructing genomes from metagenomic data.
Docker hub: https://hub.docker.com/r/metabat/metabat and its home page: https://bitbucket.org/berkeleylab/metabat/src/master/
Link to section 'Versions' of 'metabat' Versions
- 2.15-5
Link to section 'Commands' of 'metabat' Commands
- aggregateBinDepths.pl
- aggregateContigOverlapsByBin.pl
- contigOverlaps
- jgi_summarize_bam_contig_depths
- merge_depths.pl
- metabat
- metabat1
- metabat2
- runMetaBat.sh
Link to section 'Module' of 'metabat' Module
You can load the modules by:
module load biocontainers
module load metabat
Link to section 'Example job' of 'metabat' 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 Metabat on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=metabat
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers metabat
metabat2 -m 10000 \
-t 24 \
-i contig.fasta \
-o metabat2_output \
-a depth.txt