MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. It includes an updated computational strategy to assemble mitochondrial genomes from whole exome and/or genome sequencing and an improved fragment-classify tool for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. It also provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants and a Variant Call Format file featuring allele-specific heteroplasmy.

References:

• Calabrese C, Simone D, Diroma MA, Santorsola M, Gutt C, Gasparre G, Picardi E, Pesole G, Attimonelli M. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics. 2014 Jul 14. PMID: 25028726

• MToolBox Web Site

• Module Name: mtoolbox (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mtoolbox
[user@cn3144 ~]$ cd /path/to/mtoolbox/input/dir
[user@cn3144 ~]$ MToolbox.sh -i input file 
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. mtoolbox.sh). For example:

#!/bin/bash
set -e
module load mtoolbox
cd MToolbox/input/files/dir
MToolBox.sh -i fastq -I -M -r RCRS

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] mtoolbox.sh

Create a swarmfile (e.g. mtoolbox.swarm). For example:

cd /MToolbox/input/dir1 && MToolbox.sh -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"
cd /MToolbox/input/dir2 && Mtoolbox.sh -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"
cd /MToolbox/input/dir3 && MToolbox.sh -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"
cd /MToolbox/input/dir4 && MToolbox.sh -i <input_format> -r <reference_sequence> -m "<mapExome_options>" -a "<assembleMTgenome_options>" -c "<mt-classifier_options>"

Submit this job using the swarm command.

swarm -f mtoolbox.swarm [-g #] [-t #] --module mtoolbox