porechop on Biowulf

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Porechop finds and removes adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off. Reads with adapters in its middle are treated as chimeric and split into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Reads barcoded with some barcoding kits can also be demultiplexed.

Documentation

porechop on GitHub/rrwick/Porechop

Important Notes

Module Name: porechop (see the modules page for more information)
porechop can use multiple threads to increase processing speed
Set $PORECHOP_ADAPTERS to the full path of a modified adapter.py file to replace the original adapter file for including additional adapters

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 porechop
[user@cn3144 ~]$ porechop -i input_reads.fastq.gz -o output_reads.fastq.gz
...
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job

Most jobs should be run as batch jobs.

Create a batch input file (e.g. porechop.sh), which uses the input file 'porechop.in'. For example:

#!/bin/bash
module load porechop/0.2.3 || exit 1
porechop -i input_reads.fastq.gz -b output_dir --threads=$SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 [--mem=#] porechop.sh

Swarm of Jobs

A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

porechop -i input_reads1.fastq.gz -o output_reads1.fastq.gz --verbosity 2 --threads $SLURM_CPUS_PER_TASK
porechop -i input_reads2.fastq.gz -o output_reads2.fastq.gz --verbosity 2 --threads $SLURM_CPUS_PER_TASK
porechop -i input_reads3.fastq.gz -o output_reads3.fastq.gz --verbosity 2 --threads $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f porechop.swarm [-g #] -t 6 --module porechop

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
--module porechop	Loads the porechop module for each subjob in the swarm