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Nicolas Pons INRA Institut Micalis Plateforme MetaQuant Jouy-en-Josas, France

MetaQuant A new platform dealing with DNA samples to produce metagenomic analysis . A use case for big data. Nicolas Pons INRA Institut Micalis Plateforme MetaQuant Jouy-en-Josas, France. 6th International dCache workshop. What is MetaQuant ?.

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Nicolas Pons INRA Institut Micalis Plateforme MetaQuant Jouy-en-Josas, France

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  1. MetaQuantA new platformdealingwith DNA samples to producemetagenomicanalysis.A use case for big data. Nicolas Pons INRA Institut Micalis Plateforme MetaQuant Jouy-en-Josas, France 6th International dCache workshop

  2. WhatisMetaQuant ? • Scientificleaders : Sean Kennedy and Dusko Ehrlich • DNA/RNA sequencing : Nathalie Galleron and Benoit Quinquis • (Bio)informatics: Jean-Michel Batto, Nicolas Pons and Pierre Léonard • Statistics and analysis: Emmanuelle Lechatellier and Edi Prifti Sequencing and metagenomic analysis platform dedicated to the study of the human microbiota.

  3. The human intestinal microbiotais a forgottenorgan… • 100 trillion microorganisms ; 10-fold more cellsthan the human body; 2 kg of mass! • Interface betweenfood and epithelium • In contact with the 1st pool of immune cells and the 2nd pool of neural cells of the body …witha major role in health & disease !

  4. Most of microorganisms are unknown and uncultivable… Use of Metagenomics

  5. Whatismetagenomics? Metagenome can be defined as the ensemble of genes of the microbes from a given ecological niche.Metagenomics allows to characterize composition, properties and dynamics of a microbiome by studying the metagenome.

  6. Quantitative metagenomicspipeline Mapping the short reads and counting the genes Metabolism reconstruction Stoolsample Gene abundance profiles in differentsamples Ecosystem reconstruction Statisticalanalysis & diagnostic Referencegenecatalog A powerful microscope! Geneticvariability

  7. Our sequencing production • MetaQuantplatform (since 2008) • 2SOLiD 5500xl • More than 1200 sequencedsamples • 40E9 short readsequences • 500E10 bases • 650000 files for 31 TB • HumanGenome Project (2001) • 3 years • 16 sequencingcenters • 22E9 bases

  8. Our analysis pipeline : Meteor 250GB 24 files Primary data evolution Per week 1TB ~20000 files

  9. Our data managmentsystem : iMOMi Samples Reference • iMOMi Clusters Metadata SQL system • PostgreSQL • AdvantageDB • ZFS • NFS and Samba export Mapping SNPs Gene Profiles APP : IDDN.FR.001.080038.000.R.P.2007.000.31235 NoSQL system http://locus.jouy.inra.fr/imomi (Pons ,et al., 2008)

  10. Our othergenomethe human intestinal metagenome March 2010 3.3 million microbialgenecatalog 150-foldhumangenome

  11. Enterotypes of the humangutmicrobiome Danes n=85; Illumina Europeans, Americans, Asians. n=33; Sanger US n=154; 454 Enterotypes can be likened to blood groups but the reasons for their existence remains to be elucidated Nature, 2011

  12. ~800 metagenomicspeciesdiscoveredwith massive GPU computation • Hierarchical descendant graph & DAPC clustering • By computation of spearmancorrelation • 3.3E6 x 800  5E12correlations to calculate • With one CPU : more than a year to do it… • MetaProf • CUDA programming • 2H with 40 GPU (Titane/CCRT deployment) (Almeida et al., 2012 in preparation)

  13. MetaQuantworkswell, but…

  14. MetaQuant…

  15. … to MetaGenoPolis • Pre-industrialdemonstratorlaunchedat INRA in 2012 On the way of the Petabyte !!! dCachecouldbe the solution

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