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
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 7 patients (33 points) IGH 6 patients (25 points)
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 Lille sequencing platform TRG 7 patients (33 points) IGH 6 patients (25 points)
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 Lille sequencing platform TRG 7 patients (33 points) IGH 6 patients (25 points)
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 Lille sequencing platform TRG 7 patients (33 points) IGH 6 patients (25 points)
Previously: focusing on one clone CC BY NC SA heyitsgarrett
Now, with NGS: Visualizing a population! CC BY NC SA heyitsgarrett
“Converting” sequences in cows Sequences
“Converting” sequences in cows ? Sequences
“Converting” sequences in cows ? Sequences
Fingerprint = window over CDR3 Window Sequence CDR3
Fingerprint = window over CDR3 Window Sequence CDR3
Fingerprint = window over CDR3 Window V J Sequence CDR3
A quick preprocessing to segmentation 1 =
A quick preprocessing to segmentation 1 = 1 , 000 , 000 sequences < 1 min.
A quick preprocessing to segmentation 1 = 1 , 000 , 000 sequences < 1 min. Representative sequence Detailed segmentation
Vidjil: browse through the diversity Allow anyone to view its data Data from Abracadabra pipeline or Vidjil or. . . Available online at ❤tt♣✿✴✴✈✐❞❥✐❧✳♦r❣✴❜r♦✇s❡r Ask for login and password. Sample data at ❤tt♣✿✴✴✈✐❞❥✐❧✳♦r❣✴❜r♦✇s❡r✴s❛♠♣❧❡ Free software
In Rotterdam, last October CC BY SA Achrwiki Wikimedia Commons
Easing the understanding of the data
Easing the understanding of the data Comparing samples MRD: Follow-up points QC: labs
Easing the understanding of the data Comparing samples MRD: Follow-up points QC: labs Studying a sample
Easing the understanding of the data Comparing samples MRD: Follow-up points QC: labs Studying a sample Analyzing sequences Alignments, IMGT/V-QUEST. . .
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 :-)
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 :-)
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 :-)
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 :-)
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