nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more

• nanopolish Main Site

• Module Name: nanopolish (see the modules page for more information)
• Multithreaded app (use -t option; not available in all commands)
• Environment variables set
  • NANOPOLISH_TESTDATA
• Example files in /usr/local/apps/nanopolish/TEST_DATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem 4g
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 nanopolish

[user@cn3144 ~]$ cp $NANOPOLISH_TESTDATA/* .

[user@cn3144 ~]$ tar -xf ecoli_2kb_region.tar.gz

[user@cn3144 ~]$ cd ecoli_2kb_region/

[user@cn3144 ~]$ nanopolish index -d fast5_files/ reads.fasta
[readdb] indexing fast5_files/
[readdb] num reads: 112, num reads with path to fast5: 112

[user@cn3144 ~]$ nanopolish
error: no command provided
usage: nanopolish [command] [options]
  valid commands: 
    --help
    --version
    call-methylation
    eventalign
    extract
    getmodel
    help
    index
    methyltrain
    phase-reads
    polya
    scorereads
    variants
    vcf2fasta
  for help on given command, type nanopolish command --help

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

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

#!/bin/bash
set -e
module load nanopolish
nanopolish index -d fast5_files/ reads.fasta

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=4g nanopolish.sh

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

nanopolish index -d fast5_files1/ reads1.fasta
nanopolish index -d fast5_files2/ reads2.fasta
nanopolish index -d fast5_files3/ reads3.fasta

Submit this job using the swarm command.

swarm -f nanopolish.swarm -g 4 -t 2 --module nanopolish