Summary

Vidjil – Documentation

The Vidjil team (2026: Florian, Guillaume, Lou, Mathieu, Mikaël, Sami)

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.

Life scientist

We advise new users to run through to the tutorial to have an overview of Vidjil.

Tutorial "Mastering the Vidjil web application": web version // pdf, to print

• Part 1: Dealing with samples/patients/runs, controlling quality. For organizing samples/database
• Part 2 : Browsing and anlyzing clones in one sample. First-time users can directly start here to get to know Vidjil features
• Part 3: Analyzing multiple samples, exporting data. This should be done after Parts 1 and 2.

Full documentation

• Web platform main user manual.
• Libraries and recombinations, documentation on library preparation and sequencing as well on detected immune recombinations
• Spike-in normalization

Organizational topics

• Demo access 🔗 to the patient, experiment and sample public test server
• Hosting options and healthcare compliance
• Privacy policy and GDPR compliance

Bioinformatician

• Vidjil-algo documentation, usage from the command-line
• fuse.py, converting and merging immune repertoire data
• server API, for batch interaction with a vidjil server
• 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 administrator

• 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 development quality, including software engineering methods and human and team processes
• Bioinformatics, technical, and administrative Roadmap
• Public datasets 🔗 supporting Vidjil publications
• Credits, references
• Open-source and licensing

Further developer documentation

These documentations and additional developer and maintainer documentation are available from the doc/ directory in the source files.

• Algorithm
• Germlines
• Web client
• Web server

Changelogs

New features, improvements, and bug fixes are listed in the following files.

• Vidjil-algo
• Vidjil client and server
• Docker

Further help

Further help can always be asked to contact@vidjil.org. We can also arrange phone or video meeting.