Vidjil – Documentation
The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
Vidjil is an open-source platform for the analysis of high-throughput sequencing data from lymphocytes. V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up. With adapted library preparation and sequencing, high-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated sequencing methods and software, called either Rep-Seq or AIRR-Seq.
- Tutorial "Mastering the Vidjil web application": english (pdf) 🔗. Start by this tutorial to have an overview of Vidjil.
- Web platform user manual. This is the main user manual of the Vidjil platform.
- Libraries and recombinations, documentation on library preparation and sequencing as well on detected immune recombinations
- Demo access 🔗 to the patient, experiment and sample public test server
- Hosting options and healthcare compliance
- Vidjil-algo documentation, usage from the command-line
- fuse.py, converting and merging immune repertoire data
- Specification of the .vidjil format to encode immune repertoires with clones with V(D)J recombinations
- Specification of the warnings, list of default tags
- Specification of the .should-vdj.fa tests for encoding and testing curated V(D)J designations
- Server administration (web), configuration and administration features available from the web application
- Server installation and maintenance (docker), server installation, configuration and maintenance from the command line
Quality, open data, roadmap, credits
- Software and developement quality, including software engineering methods and human and team processes
- Bioinformatics, technical, and administrative Roadmap
- Public datasets 🔗 supporting Vidjil publications
- Credits, references
Further developer documentation
These documentations and additional developer and maintainer documentation
are available from the doc/ directory in the source files,
including development notes on Vidjil-algo (
dev-algo.md), on the germlines (
on the web application client (
dev-client.md), and on the server (
Further help can always be asked to firstname.lastname@example.org. We can also arrange phone or video meeting.