Pierre Peterlongo

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

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

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)

• Document principal
• Publications majeures associées

Slides (english)

• slides

Video (french)

Je soutiens publiquement mon HDR le lundi 25 janvier.

C’est à l’IRISA/Inria, en salle Métivier à 14h.

Soyez les bienvenus.

A new discoSnp++ release is available. http://colibread.inria.fr/software/discosnp/

Existing features in a few words

• Detect SNPs and indels from raw read set(s), without the need of a reference genome.
• Provides genotyping and ranking
• Generates a fasta file of variant predictions containing a micro-assembly of the variant left and rigth neighbors
• Generates a VCF of predicted variants
  • Without a reference: no informative prediction locus
  • Providing a reference sequence: map predictions. The VCF contains mapping information (locus, multiple matches, …)
• Fast, low memory footprint, easy to use.

New features

• New input format (using file of files)
  • Easier to deal with paired datasets
  • Easier to simulate file concatenation
• The reference can also be used for calling predictions (not only for mapping them)
• The coverage thresholds can be
  • set separately for each read set
  • and/or automatically detected for each set

Any comment / remark positive or not is still warmly welcome on the biostar forum

Björn Grüning developped a  Galaxy Docker repository for metagenomics including commet : https://github.com/bgruening/galaxy-metagenomics

Information and download: DiscoSnp++ page

The discoSnp paper will soon be published in Nucleic Acid Research. PDF proofs are already available from the discoSnp home page. discoSnp

We’re happy to announce that commet will soon be presented at the bibm 2014 conference.