Megahit

Introduction

Megahit is a ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

For more information, please check its website: https://biocontainers.pro/tools/megahit and its home page on Github.

Versions

1.2.9

Commands

megahit

Module

You can load the modules by:

module load biocontainers
module load megahit

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 Megahit on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=megahit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers megahit

megahit --12 SRR1976948.abundtrim.subset.pe.fq.gz,SRR1977249.abundtrim.subset.pe.fq.gz -o combined