routine-nanopore-processing

A set of scripts to support routine processing of Oxford Nanopore MinION sequence data on a Sun GridEngine-based HPC cluster.

Getting Started

Prepare conda environments

It is expected that several bioinformatics tools are provided as tool-specific conda environments. Each environment is activated in turn by calling:

source activate <tool-version>

...and deactivated by calling:

source deactivate

In order for this to work, a conda installation must be available on the user's PATH.

If these environments are not already available on your system, create them as follows:

conda create -n <tool-version> tool=version

For example:

conda create -n mash-2.0 mash=2.0

Edit the config.conf file

A config.conf file is used to customize these scripts to a specific system. Review that file and fill in appropriate values for those settings before running these scripts.