ig_graph

IgGraph performs VDJ classification of antibody reads using the colored antibody graph (i.e., a colored de Bruijn graph).

http://sbonisso.github.io/ig_graph/

Dependencies

• gcc with C++11 support GCC 4.7 and later
• SeqAn 2.0+
• TCLAP
• cereal
• catch

IgGraph has been tested on many different versions of Ubuntu, Mac OS X, and should work on most unix-based OSs. If building from source the dependencies listed are contained as subtrees in the git repository, so there is no need to install them separately.

Compilation

Clone the repository, all dependencies are contained as subtrees, so nothing special needs to be done. Alternatively, you can also download the tar/zip and build from those.

git clone https://github.com/sbonisso/ig_graph.git

Compile by running make in the top-level directory.

cd ig_graph
make

To create tests, additionally run make test.

make test
./unit_test

Use

The iggraph executable can be run directly, or for simplicity, you can use the two runiggraph{hsap,mmus}.sh scripts, from inside the ig_graph directory, to run for either human or mouse.

./run_iggraph_hsap.sh --read_file igseq_reads.fa \
              --output_file igseq_vdj.tsv \
              --num_thread 4

The options and flags can be seen when running the built-in help:

./iggraph -h