nanopack is a collection of long read processing and analysis tools created by Wouter De Coster and Rosa Rademakers. It includes the following tools:

• NanoPlot: creates relevant plots derived from reads (fastq), alignments (bam) and albacore summary files.
• NanoComp: compares multiple runs on read length and quality based on reads (fastq), alignments (bam) or albacore summary files.
• NanoQC: generates plots to investigate nucleotide composition and quality distribution at the end of reads.
• Cramino: generates summary of BAM or CRAM files.
• chopper: a tool for filtering, trimming, and removing contaminants
• phasius: creates a graphical representation of the read phasing performance (from BAM/CRAM files)

References:

• Wouter De Coster, Rosa Rademakers. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics, Volume 39, Issue 5, May 2023, btad311.

• nanopack GitHub

• Module Name: nanopack (see the modules page for more information)
• Multithreaded
• This application produces HTML reports and image files. You can use hpcdrive to view these reports on your local workstation.
• Test data from nanotest respository can be accessed using NANOPACK_TEST_DATA environment variable

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 nanopack

[user@cn3144 ~]$ cd /data/$USER

[user@cn3144 user]$ cp -r $NANOPACK_TEST_DATA .

[user@cn3144 user]$ cd nanotest

[user@cn3144 nanotest]$ NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed

[user@cn3144 nanotest]$ cramino alignment.bam
File name       alignment.bam
Number of alignments    1115
% from total reads      90.14
Yield [Gb]      0.01
Mean coverage   2.17
Yield [Gb] (>25kb)      0.00
N50     19271
N75     10270
Median length   6895.00
Mean length     11070
Median identity 90.84
Mean identity   89.96
Path    alignment.bam

[user@cn3144 nanotest]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load nanopack
cd /data/$USER/reads
NanoComp -t $SLURM_CPUS_PER_TASK \
    --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz \
    --names run1 run2 run3 run4

Submit this job using the Slurm sbatch command.

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

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

zcat reads1.fastq.gz | chopper --tailcrop 10 | gzip > reads1_trimmed.fastq.gz
zcat reads2.fastq.gz | chopper --tailcrop 10 | gzip > reads2_trimmed.fastq.gz
zcat reads3.fastq.gz | chopper --tailcrop 10 | gzip > reads3_trimmed.fastq.gz
zcat reads4.fastq.gz | chopper --tailcrop 10 | gzip > reads4_trimmed.fastq.gz

Submit this job using the swarm command.

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