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:
BioContainers: https://biocontainers.pro/tools/megahit
Home page: https://github.com/voutcn/megahit

Versions

1.2.9

Commands

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=megahit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load megahit/XXXX ### you can run *module avail megahit* to check all available versions

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