Immune Repertoire Analysis
with Vidjil

Everywhere in the world, 28 September 2020
Paris, 29 September 2020

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. High-throughput sequencing (NGS/HTS) now enables the deep sequencing of lymphoid populations. With dedicated AIRR-Seq/Rep-Seq bioinformatics methods and software, clinicians and researchers can now qualify and sometimes quantify the heterogeneity of these lymphoid populations.

The Vidjil platform is used in routine clinical practice in hospitals around the world, in particular for the diagnosis of patients suffering Acute Lymphoblastic Leukemia (ALL). More than 8,000 samples of ALL patients were analyzed with Vidjil since 2015. Vidjil is also used in several studies on hemopathies (ALL, CLL, lymphomas, WM...) as well as on immunology topics involving T-cell or B-cell repertoires.

This workshop is intended for users and developers of Vidjil, to discover the platform, share experience, to raise questions and possibly to set up new collaborations between biologists and bioinformaticians. Due to outbreak of Covid-19, we will organize a full workshop in Paris in 2021 with more talks. This 2020 special edition will allow everyone to have a introductive tutorial/training with practical hands-on sessions. The Vidjil Workshop takes place every 18 months. The previous workshops (2016, 2017, 2019) gathered at each edition between 30 and 40 scientists from 5 to 7 countries.


Monday 28 September, all-remote day, in English

10:00 – 11:30 Remote talks: Algorithmics and bioinformatics, an introduction to the Vidjil platform
  • Mathieu Giraud and Mikaël Salson (Lille), Fast and efficient clonal analysis of reads with Ig/TR recombinations
  • Florian Thonier (Rennes), Marc Duez (Lille), The Vidjil web platform for RepSeq data: presentation, 2020 news
  • The VidjilNet consortium: Why and how?
11:30 – 13:00 Remote Practical Session 1
  • Usage of the Vidjil Web platform, analysis of participant and/or public data
  • (both tutorial and advanced usage)
  • Private remote meetings on participant data
15:00 – 18:00 Remote Practical Session 2

Tuesday 29 September, physical meeting in Paris, en français

10:30 – 13:00 Session pratique 3
14:00 – 16:30 Discussion entre laboratoires utilisateurs

There are thus two options to participate to the practical sessions, that will have the same content. The participants can work on their computer either remotely (Monday) or in Paris, by bringing own's laptop (Tuesday). You can also upload your own NGS data (fasta / fastq / fastq.gz files), into user accounts on before the workshop. We also provide public test data for the people who do not currently have their own NGS Rep-Seq data.


The workshop is sponsored by the VidjilNet consortium at Inria and the GBMHM. There is no registration fee, but, for organization purposes, we ask you to register. To register, please copy, paste and fill the following lines into an email to Florian, Marc, Mathieu and Mikaël :

First name: 
Last name: 
I will be present:

    [ ] Monday 28 September, remotely, 10:00 – 11:00, for the general introduction
    [ ] Monday 28 September, remotely, for the rest of the day (formation/tutorial)

My usage of Vidjil:
    [ ] I use Vidjil at least once a month
    [ ] I use Vidjil occasionnaly
    [ ] I am a new user or I don't use Vidjil

The registration for the Tuesday (in Paris) is closed. It is still possible to register for the remote workshop on Monday.

Practical information

If a physical workshop is possible, it will take place in Paris, in the Hôpital Saint Louis, very close to the Gare de l'Est (and Gare du Nord) train stations.


The workshop is organized by Marc Duez, Mathieu Giraud, Mikaël Salson, Florian Thonier, from CRIStAL, Inria Lille and the VidjilNet consortium, and by Carole Maute, from GBMHM.