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.

• porechop on GitHub/rrwick/Porechop

• Module Name: porechop (see the modules page for more information)
• porechop can use multiple threads to increase processing speed

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 ~]$

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

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