- Publications Hal
- Indexer des milliards d’éléments avec les filtres de Bloom
- Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA
- kmindex and ORA: indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets
- fimpera: drastic improvement of Approximate Membership Query data-structures with counts
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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 … Continuer la lecture
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Habilitation à diriger les recherches.
Je soutiens publiquement mon HDR le lundi 25 janvier. C’est à l’IRISA/Inria, en salle Métivier à 14h. Soyez les bienvenus.
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DiscoSnp++2.2.0 released
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 … Continuer la lecture
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Galaxy Docker repository for metagenomics
Björn Grüning developped a Galaxy Docker repository for metagenomics including commet : https://github.com/bgruening/galaxy-metagenomics
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B-GREAT: map short reads on de-bruijn graph
First formal proposal analysing the problem of mapping short reads on a de Bruijn graph: complexity analysis, heuristic algorithm and test results here: http://arxiv.org/abs/1505.04911
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DiscoSnp++ now genotypes results and provides a VCF file
From version 2.1.2, discoSnp++ includes several new features as the usage of paired reads, the creation of a genotype or the production of a VCF with or without the use of a reference genome. Info and downloads : discoSnp++ page
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DiscoSnp becomes DiscoSnp++. Detect SNPs and more
Information and download: DiscoSnp++ page
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Paper discoSnp published in NAR
The discoSnp paper will soon be published in Nucleic Acid Research. PDF proofs are already available from the discoSnp home page. discoSnp
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Paper commet accepted to bibm 2014
We’re happy to announce that commet will soon be presented at the bibm 2014 conference.
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