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Nanopolish
Overview
Nanopolish is a Software package for signal-level analysis of Oxford Nanopore sequencing data. The application is written in C++ and can be used in batch or interactively (via the qrsh command).
- Version 0.9.0 is installed on the CSF.
- Version 0.8.4 is installed on the DPSF.
Restrictions on use
There are no restrictions on using this software on the CSF. The application is released under the MPL license.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/nanopolish/0.9.0
Running the application
Please do not run nanopolish on the login node. Jobs should be submitted to the compute nodes via batch or run interactively via the qrsh command.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings nanopolish [command] [options]
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Interactive use of the GUI
FastQC can be run interactively but this must not be run on the login node. Instead you must schedule an interactive session on a compute node. Use the following commands (after loading the modulefile):
qrsh -l inter -l short -V nanopolish
This will only run when a free core is available on one of the interactive nodes. If no free resources are available you will be asked to try again later.
Further info
- Brief notes on command-line flags are available on the CSF using:
nanopolish --help
Updates
None.