Metabat¶
Introduction¶
Metabat
is a robust statistical framework for reconstructing genomes from metagenomic data.
For more information, please check its | Docker hub: https://hub.docker.com/r/metabat/metabat and its home page: https://bitbucket.org/berkeleylab/metabat/src/master/
Versions¶
2.15-5
Commands¶
aggregateBinDepths.pl
aggregateContigOverlapsByBin.pl
contigOverlaps
jgi_summarize_bam_contig_depths
merge_depths.pl
metabat
metabat1
metabat2
runMetaBat.sh
Module¶
You can load the modules by:
module load biocontainers
module load metabat
Example job¶
Warning
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