Megan

Introduction

Megan is a computer program that allows optimized analysis of large metagenomic datasets. Metagenomics is the analysis of the genomic sequences from a usually uncultured environmental sample.

Versions

  • 6.21.7

Commands

  • MEGAN

  • blast2lca

  • blast2rma

  • daa2info

  • daa2rma

  • daa-meganizer

  • gc-assembler

  • rma2info

  • sam2rma

  • references-annotator

Module

You can load the modules by:

module load biocontainers
module load megan

GUI

To run MEGAN with GUI, it is recommended to run within ThinLinc:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers megan
(base) UserID@bell-a008:~ $ MEGAN
../../_images/megan.png

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 Megan on our clusters:

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

module --force purge
ml biocontainers megan