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).

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

See which versions of igdiscover are available:

$ module avail igdiscover

Load one version into your environment and run it:

$ module load igdiscover/0.12.3
$ igdiscover --help

Notes from the sysadmin during installation:

$ 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

Run the test data:

$ 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