Mitofinder

Introduction

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

For more information, please check its website: https://cloud.sylabs.io/library/remiallio/default/mitofinder and its home page on Github.

Versions

• 1.4.1

Commands

• mitofinder

Module

You can load the modules by:

module load biocontainers
module load mitofinder

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 Mitofinder on our clusters:

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

module --force purge
ml biocontainers mitofinder

mitofinder -j Aphaenogaster_megommata_SRR1303315 \
           -1 Aphaenogaster_megommata_SRR1303315_R1_cleaned.fastq.gz \
           -2 Aphaenogaster_megommata_SRR1303315_R2_cleaned.fastq.gz \
           -r reference.gb -o 5 -p 5 -m 10