Software: Mitofinder
Description
Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.
Available Versions
| Unspecified: | 1.4.1 |
|---|
For more information, please check its website: https://cloud.sylabs.io/library/remiallio/default/mitofinder and its home page on Github.
Commands
- mitofinder
Module
You can load the modules by:
module load biocontainers
module load mitofinder
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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