====== IgDiscover ======

IgDiscover analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes).

===== Information =====

  * Version: 0.12.3
  * Added: April, 2020
  * Link: http://docs.igdiscover.se/en/stable/index.html

===== Usage =====

See which versions of igdiscover are available:
<code>$ module avail igdiscover</code>

Load one version into your environment and run it:
<code>$ module load igdiscover/0.12.3
$ igdiscover --help</code>

Note: parts of the IgDiscover pipeline seem to use all the CPUs on the current host with no option to control the number of parallel threads. If you know how to limit this please write to me so I can update this note!

===== Installation ======

Notes from the sysadmin during installation:

<code>
$ module load python/3.7
$ sudo mkdir -p /export/apps/igdiscover/0.12.3
$ sudo chown aorth /export/apps/igdiscover/0.12.3
$ python -m venv /export/apps/igdiscover/0.12.3
$ source /export/apps/igdiscover/0.12.3/bin/activate
$ pip install --upgrade pip setuptools
$ pip install igdiscover
$ sudo chown -R root:root /export/apps/igdiscover/0.12.3
</code>

Run the [[http://docs.igdiscover.se/en/stable/testing.html#test|test data]]:

<code>$ module load igdiscover/0.12.3
$ cd /tmp
$ wget https://bitbucket.org/igdiscover/testdata/downloads/igdiscover-testdata-0.5.tar.gz
$ tar xvf igdiscover-testdata-0.5.tar.gz
$ igdiscover init --db igdiscover-testdata/database/ --reads igdiscover-testdata/reads.1.fastq.gz discovertest
$ cd discovertest && igdiscover run</code>