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This repository is for an old IgDiscover version. Please see the new repository at https://gitlab.com/gkhlab/igdiscover22/ or the homepage at https://www.igdiscover.se/ for the most recent and maintained IgDiscover version. |
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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
