Bwise presentation – Sequencing, Finishing, and Analysis in the Future

Bwise was presented during the workshop « Sequencing, Finishing, and Analysis in the Future »

Slides are available on my « presentation page »

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NEW minimal perfect hash library BBHASH

A preprint for our minimal perfect hash library BBHash (formerly BooPHF) is up on arxiv ( ).

Screen Shot 2017-02-13 at 08.47.58

 

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New Short Read Connector Release

A new release (1.0.1) of the RConnector tool (connecting reads from large datasets) is available here.

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Slides from the colib’read workshop available

You may find all slides from the colib’read workshop on the program page.

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Workshop Colib’Read – Program Online

The Colib’read workshop program is now online on this page http://gdr-bim.cnrs.fr/colibread/program/.

We remind you that the attendance is free but ***registration is mandatory*** see website: http://gdr-bim.cnrs.fr/colibread/.
Note that space is limited, and registration will be taken in the order received.

— WHAT —
Calling biological information from raw reads and long reads correction. All methods are reference free.

— HOW —
The workshop is composed of overview and practical talks, of success stories (bioanalyses results), of tools demonstrations and of interactive discussions.

— WHEN —
November 7,8 2016

— LANGUAGE —
English

— WHERE —
Institut Curie – Amphithéâtre Constant Burg  12, Rue Lhomond 75005 Pari

— REGISTRATION —
The workshop attendance is free but ***registration is mandatory*** (see website)

— WEB SITE —
http://gdr-bim.cnrs.fr/colibread/

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Short Read Connector presentation

Short Read Connector was published and presented during the Prague Stringology Conference 2016.

Slides available from my presentation page.

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Simka presentation

Simka (de novo metagenomics comparisons) was presented during the « Pasteur Metagenomics Summer School« .

Check the presentation page.

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Workshop colib’read – November 7,8 2016

The colib’read group (http://colibread.inria.fr/) organises a workshop which aim is to present tools and results obtained for “calling biological information from raw reads”. The tools developed by the group are efficient both in terms of memory and computing time.
Most of these tools are reference-free and assembly-free, and thus give the possibility to analyse reads without a reference genome or without performing de novo assembly.
The methods we developed can readily be used to find variants in the context of non-model species, where no (good) reference genome is available, but we also would like to promote their use in the context of model species, especially in disease conditions.

Presentations will include a taste of algorithmic and will show some applications and results obtained using our proposed tools, such as kissplice [1], discoSnp [2] or Lordec [3]. We will also propose some interactive tool demonstrations and the program will include time for discussions.

[1] http://kissplice.prabi.fr
[2] http://colibread.inria.fr/software/discosnp
[3] http://www.atgc-montpellier.fr/lordec/

— WHEN —
November 7,8 2016

— WHERE —
Institut Curie – Amphithéâtre Constant Burg  12, Rue Lhomond 75005 Pari

— REGISTATION —
The workshop attendance is free but ***registration is mandatory*** (see website)

— WEB SITE —
http://gdr-bim.cnrs.fr/colibread/

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New datastructure and applications for kmer indexing

Paper submited: http://arxiv.org/abs/1605.08319

Indexing billions kmers with frugal computation time and memory fingerprint + applications examples

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HDR – thesis habilitation

I defended my thesis habilitation on january 25, 2016.

The jury was:

  • Hélène Touzet –Reviewer –Research Director, Inria Lille
  • Sophie Schbath – Reviewer –Research Director, INRA, Jouy-en-Josas
  • Gunnar Klau – Reviewer – Professor, CWI Amsterdam
  • Alain Viari – Inria Lyon – Research Director
  • Philippe Vandenkoornhuyse – Professor Rennes1 university
  • Guillaume Blin – Professor, Bordeaux university

Documents (french)

Slides (english)

Video (french)

  • To be announced
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