Singlem

Introduction

SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.

For more information, please check:

Docker hub: https://hub.docker.com/r/wwood/singlem

Home page: https://github.com/wwood/singlem

Versions

• 0.13.2

Commands

• singlem

Module

You can load the modules by:

module load biocontainers
module load singlem

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 singlem on our clusters:

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

module --force purge
ml biocontainers singlem