Filtering and trimming for long-read sequencing data (PacBio/ONT). Filtering is done on average read quality and minimal or maximal read length, and applying a headcrop (start of read) and tailcrop (end of read) while printing the reads passing the filter.

• chopper Main Site

• Module Name: chopper (see the modules page for more information)
• Multithreaded by use of -t/--threads arguments
• Environment variables set
  • CHOPPER_HOME
• Example files in $CHOPPER_HOME/test

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 chopper
[user@cn3144 ~]$ chopper --threads 2 -q 10 -l 500 < $CHOPPER_HOME/test/test.fastq | gzip > filtered.fastq.gz
Kept 205 reads out of 250 reads
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load chopper
chopper -q 10 -l 500 < $CHOPPER_HOME/test/test.fastq | gzip > filtered.fastq.gz

Submit this job using the Slurm sbatch command.

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

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

gunzip -c sample1.fq.gz | chopper -q 10 -l 500 | gzip > sample1.filtered.fq.gz
gunzip -c sample2.fq.gz | chopper -q 10 -l 500 | gzip > sample2.filtered.fq.gz
gunzip -c sample3.fq.gz | chopper -q 10 -l 500 | gzip > sample3.filtered.fq.gz
gunzip -c sample4.fq.gz | chopper -q 10 -l 500 | gzip > sample4.filtered.fq.gz

Submit this job using the swarm command.

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