Maxbin2

Introduction

Maxbin2 is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

For more information, please check:
Docker hub: https://hub.docker.com/r/nanozoo/maxbin2
Home page: https://sourceforge.net/projects/maxbin2/

Versions

  • 2.2.7

Commands

  • run_MaxBin.pl

  • run_FragGeneScan.pl

Module

You can load the modules by:

module load biocontainers
module load maxbin2

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 maxbin2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=maxbin2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers maxbin2

run_MaxBin.pl -contig subset_assembly.fa \
     -abund_list abundance.list -max_iteration 5 -out mbin