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 National Bioinformatics Infrastructure Sweden at Science for Life Laboratory (SciLifeLab).
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
