Dear fellow Bioinformaticians,
I would like to introduce VDJtools, a recently published software for post-analysis of immune repertoire sequencing (Rep-Seq) data. Rep-seq technology allows profiling antigen receptors of T- and B-cells in the sample of interest and has numerous applications ranging from searching for T-cells specific for cancer antigens in tumor-infiltrating lymphocyte populations to reconstructing the state of entire adaptive immune system of an individual. The data produced by Rep-Seq is highly complex due to the vast diversity of possible immune receptor variants. Compared to conventional metagenomics, the number of possible variants is several orders of magnitude higher with only a minority of so-called "public" variants that have some functional annotation.
While there many tools for processing and mapping Rep-Seq data have been published recently (see http://omictools.com/rep-seq-c424-p1.html), there is still a lack of software for post-analysis of Rep-Seq results. VDJtools software aims at filling this gap by providing a rich set of post-analysis routines extensively tested using real-world datasets coming from studies performed by our group and our collaborators.
Feature list at a glance:
- Parsers for 7 commonly used Rep-Seq processing software
- Modules implementing 23 commonly performed analysis tasks: basic repertoire statistics, diversity analysis, repertoire overlap and clustering and clonotype tracking
- Comprehensive tabular output and optimized graphical output using R
Related links:
- The paper: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004503
- Software source and binaries: https://github.com/mikessh/vdjtools
- Documentation: http://vdjtools-doc.readthedocs.org/en/latest/
- Real-world datasets used in benchmarking: https://github.com/mikessh/vdjtools-examples
