Vidjil: analysing HTS data from a lymphocyte population Marc Duez, - - PowerPoint PPT Presentation

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Mar 05, 2023 347 likes •619 views

Vidjil: analysing HTS data from a lymphocyte population Marc Duez, Mikal Salson, Mathieu Giraud Bonsai bioinformatics Sabine Quief, Cline Villenet, Martin Figeac Lille sequencing platform Aurlie Caillault, Nathalie Grardel, Claude

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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

SLIDE 2

Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing

Where does that come from?

Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist

MRD

TRG 7 patients (33 points) IGH 6 patients (25 points)

SLIDE 3

Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing

Where does that come from?

Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist

Lille Hospital Lille sequencing platform

MRD

TRG 7 patients (33 points) IGH 6 patients (25 points)

SLIDE 4

Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing

Where does that come from?

Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist

Lille Hospital Lille sequencing platform

MRD

TRG 7 patients (33 points) IGH 6 patients (25 points)

SLIDE 5

Bonsai bioinformatics (U. Lille 1, CNRS, Inria) Expertise in text algorithms and NGS data processing

Where does that come from?

Marc, full-time engineer Mathieu, research scientist Mikaël, research scientist

Lille Hospital Lille sequencing platform

MRD

TRG 7 patients (33 points) IGH 6 patients (25 points)

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CC BY NC SA heyitsgarrett

Previously: focusing on one clone

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CC BY NC SA heyitsgarrett

Now, with NGS: Visualizing a population!

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“Converting” sequences in cows

Sequences

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“Converting” sequences in cows

Sequences

?

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“Converting” sequences in cows

Sequences

?

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Window

Fingerprint = window over CDR3

Sequence CDR3

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Window

Fingerprint = window over CDR3

Sequence CDR3

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Window

Fingerprint = window over CDR3

Sequence CDR3 V J

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A quick preprocessing to segmentation

=

1

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A quick preprocessing to segmentation

=

1 1, 000, 000 sequences

< 1 min.

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A quick preprocessing to segmentation

=

1 1, 000, 000 sequences

< 1 min.

Representative sequence Detailed segmentation

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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

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CC BY SA Achrwiki Wikimedia Commons

In Rotterdam, last October

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Easing the understanding of the data

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Easing the understanding of the data

Comparing samples

MRD: Follow-up points QC: labs

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Easing the understanding of the data

Comparing samples

MRD: Follow-up points QC: labs

Studying a sample

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Easing the understanding of the data

Comparing samples

MRD: Follow-up points QC: labs

Studying a sample Analyzing sequences

Alignments, IMGT/V-QUEST. . .

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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 :-)

SLIDE 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 :-)

SLIDE 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 :-)

SLIDE 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 :-)