Vidjil: analysing HTS data from a lymphocyte population
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1 Vidjil: analysing HTS data from a lymphocyte population Marc Duez, Mikaël Salson, Mathieu Giraud Bonsai bioinformatics Sabine Quief, Céline Villenet, Martin Figeac Lille sequencing platform Aurélie Caillault, Nathalie Grardel, Claude Preudhomme Hematology department, Lille hospital Work supported by Région Nord-Pas-de-Calais and SIRIC OncoLille
2 Where does that come from? Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist MRD TRG IGH 7 patients (33 points) 6 patients (25 points)
3 Where does that come from? Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist MRD Lille Hospital TRG IGH 7 patients (33 points) 6 patients (25 points) Lille sequencing platform
4 Where does that come from? Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist MRD Lille Hospital TRG IGH 7 patients (33 points) 6 patients (25 points) Lille sequencing platform
5 Where does that come from? Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist MRD Lille Hospital TRG IGH 7 patients (33 points) 6 patients (25 points) Lille sequencing platform
6 Previously: focusing on one clone CC BY NC SA heyitsgarrett
7 Now, with NGS: Visualizing a population! CC BY NC SA heyitsgarrett
8 Converting sequences in cows Sequences
9 Converting sequences in cows? Sequences
10 Converting sequences in cows? Sequences
11 Fingerprint = window over CDR3 Window Sequence CDR3
12 Fingerprint = window over CDR3 Window Sequence CDR3
13 Fingerprint = window over CDR3 Sequence V Window CDR3 J
14 A quick preprocessing to segmentation = 1
15 A quick preprocessing to segmentation = 1 1, 000, 000 sequences < 1 min.
16 A quick preprocessing to segmentation = 1 1, 000, 000 sequences < 1 min. Representative sequence Detailed segmentation
17 Vidjil: browse through the diversity Allow anyone to view its data Data from Abracadabra pipeline or Vidjil or... Available online at Ask for login and password. Sample data at Free software
18 In Rotterdam, last October CC BY SA Achrwiki Wikimedia Commons
19 Easing the understanding of the data
20 Easing the understanding of the data Comparing samples MRD: Follow-up points QC: labs
21 Easing the understanding of the data Comparing samples MRD: Follow-up points QC: labs Studying a sample
22 Easing the understanding of the data Comparing samples MRD: Follow-up points QC: labs Studying a sample Analyzing sequences Alignments, IMGT/V-QUEST...
23 What s to come? Several sequencing runs in French hospitals Make Vidjil standalone Upload your data, have a coffee, see the results of the Abracadabra pipeline Strengthen the collaboration with EC-NGS, with Nikos and Vojtech Both on visualisation and on bioinformatics pipeline What you ll ask! We may not say yes to everything :-)
24 What s to come? Several sequencing runs in French hospitals Make Vidjil standalone Upload your data, have a coffee, see the results of the Abracadabra pipeline Strengthen the collaboration with EC-NGS, with Nikos and Vojtech Both on visualisation and on bioinformatics pipeline What you ll ask! We may not say yes to everything :-)
25 What s to come? Several sequencing runs in French hospitals Make Vidjil standalone Upload your data, have a coffee, see the results of the Abracadabra pipeline Strengthen the collaboration with EC-NGS, with Nikos and Vojtech Both on visualisation and on bioinformatics pipeline What you ll ask! We may not say yes to everything :-)
26 What s to come? Several sequencing runs in French hospitals Make Vidjil standalone Upload your data, have a coffee, see the results of the Abracadabra pipeline Strengthen the collaboration with EC-NGS, with Nikos and Vojtech Both on visualisation and on bioinformatics pipeline What you ll ask! We may not say yes to everything :-)
TCRG TCRA/D IGH IGK/L
Assays immunoseq Assay The inquiry to insight solution for profiling T- and B-cell s Immunosequencing solutions for multiple species and loci Illuminate the adaptive immune system with bias-controlled
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