The marginAlign package can be used to align reads to a reference genome and call single nucleotide variations (SNVs). It is specifically tailored for Oxford Nanopore Reads.

• Version: git-git-2369dafd
• Added: November, 2018
• Link: https://github.com/benedictpaten/marginAlign

See versions of marginalign that are available:

$ module avail marginalign

Load one version into your environment and run it:

$ module load marginalign/git-2369dafd
$ marginAlign

Notes from the sysadmin during installation:

$ cd /tmp
$ git clone https://github.com/benedictpaten/marginAlign.git
$ cd marginAlign
$ git submodule update --init
$ make
$ sudo mkdir -p /export/apps/marginalign/git-2369dafd
$ sudo chown aorth /export/apps/marginalign/git-2369dafd
$ virtualenv --no-site-packages --distribute /export/apps/marginalign/git-2369dafd
$ source /export/apps/marginalign/git-2369dafd/bin/activate
$ pip install --upgrade setuptools pip
$ pip install -r requirements.txt
$ cp -r LICENSE.txt margin* README.md scripts src submodules /export/apps/marginalign/git-2369dafd
$ sudo chown -R root:root /export/apps/marginalign/git-2369dafd