bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics.

• https://nanoporetech.github.io/modkit/

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

Allocate an interactive session and run the program. Sample session:

[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 modkit
[user@cn3144 ~]$ modkit pileup input_reads.bam output/path/pileup.bed --log-filepath pileup.log
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load modkit
modkit pileup input_reads.bam output/path/pileup.bed --log-filepath pileup.log

Submit this job using the Slurm sbatch command.

[user@biowulf ~]$ sbatch modkit.sh

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

modkit pileup dir1/input_reads.bam dir1/pileup.bed --log-filepath pileup1.log
modkit pileup dir2/input_reads.bam dir2/pileup.bed --log-filepath pileup2.log
modkit pileup dir3/input_reads.bam dir3/pileup.bed --log-filepath pileup3.log

Submit this job using the swarm command.

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