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