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).
IgDiscover is the result of a collaboration between the Gunilla Karlsson Hedestam group at the Department of Microbiology, Tumor and Cell Biology at Karolinska Institutet, Sweden and the Bioinformatics Long-Term Support facility at Science for Life Laboratory (SciLifeLab), Sweden.
If you use IgDiscover, please cite:
Corcoran, Martin M. and Phad, Ganesh E. and Bernat, Néstor Vázquez and Stahl-Hennig, Christiane and Sumida, Noriyuki and Persson, Mats A.A. and Martin, Marcel and Karlsson Hedestam, Gunilla B.Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.Nature Communications 7:13642 (2016)
Contents¶
- Installation
- Manual installation
- Test data set
- User guide
- Overview
- Obtaining a V/D/J database
- Input data requirements
- Configuration
- Running IgDiscover
- The analysis directory
- Format of output files
- Subcommands
- Germline and pre-germline filtering
- Data from the Sequence Read Archive (SRA)
- Does random subsampling influence results?
- Logging the program’s output to a file
- Caching of IgBLAST results and of merged reads
- Terms
- Questions and Answers
- How many sequences are needed to discover germline V gene sequences?
- Can IgDiscover analyze IgG libraries?
- Can IgDiscover analyze a previously sequenced library?
- Do the positions of the PCR primers make a difference to the output?
- What are the advantages to 5’-RACE compared to multiplex PCR for IgDiscover analysis?
- What is meant by ‘starting database’?
- How can I use the IMGT database as a starting database?
- How do I change the parameters of the program?
- Where do I find the individualized database produced by IgDiscover?
- What does the _S1234 at the end of same gene names mean?
- Advanced topics
- Development
- Changes
