Vincent Maillol (INRA) Jean-François Dufayard (CIRAD)
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1 Vincent Maillol (INRA) Jean-François Dufayard (CIRAD) Vincent Maillol, Roberto Bacilieri, Stéphanie Bocs, Jean-Michel Boursiquot, Grégory Carrier, Alexis Dereeper, Gaétan Droc, Cécile Fleury, Pierre Larmande, Loïc Le Cunff, Jean-Pierre Péros, Bertrand Pitollat, Manuel Ruiz, Gautier Sarah, Guilhem Sempéré, Marilyne Summo, Patrice This, and Jean-Francois Dufayard
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4 HPC Team Intégration Des Données, UMR AGAP HPC
5 Knowledge modeling and data integration for plant genomics Bioinformatic analysis methods for plant genomic sequences Data investigation and visualization of genomic information for plants
6 300+ permanent staff (researchers, engineers, technicians)... 6 service platforms research teams
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8 ... A large variety of tropical and mediterranean species...
9 Genetic resources Recombinations Characterize biodiversity Understand crop plants More markers... Sequencing, annotation, expression, epigenetic... Selection Detect polymorphisms of interest for agronomy Markers, QTL, association genetic Variety Facilitate new allelic combinations Assisted selection
10 Annotation and comparative genomics 1. GNPAnnot 2. GreenPhyl 3. Analysis of genome sequences 4. Comparative population genomics... Information systems 1. TropGene 2. Integrated rice functional genomics Integrated workflows 1. ESTtik 2. SNiPlay
11 Cluster (208 cores, 50 TO storage) Public databases
12 Reproducibility Cluster (208 cores, 50 TO storage) Public databases
13 Agile programming for maintenance and developments 1 session of 4 hours, every 2 weeks 6-10 developers, researchers (bioinformatic, biology), using pair programming Integration of new softwares Code maintenance, refactoring, documentation. Galaxy, bioinformatic training platform for biologists Galaxy is widely used during Southgreen trainings, as a complete replacement of command line system.
14 Vincent Maillol (INRA)
15 Designed to analyze NGS sequenced grape vines And search polymorphism between genotype
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17 Mosaik alignement filter FreeBayes Pretty FreeBayes Control coverage and depth
18 Filter sequences Mosaik alignement filter FreeBayes Pretty FreeBayes Control coverage and depth
19 Sequence alignment on a reference genome Mosaik alignement filter FreeBayes Pretty FreeBayes Control coverage and depth
20 Estimation of alignment quality Mosaik alignement filter FreeBayes Pretty FreeBayes Control coverage and depth
21 Polymorphism Search Mosaik alignement filter FreeBayes Pretty FreeBayes Control coverage and depth
22 Existing software wrapped by me Software wrapped and developed by me Mosaik alignement filter FreeBayes Pretty FreeBayes Control coverage and depth
23 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes Truncate the end of sequences Filter short sequences Filter sequence under average quality rate convert quality format
24 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes
25 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes
26 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes
27 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes
28 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes magic number ( ) 8b individual_name \0 1b nb_ref 4b Memory leak eliminate with Valgrind ansi C language Internal Framework for test driving / ref_name \0 1b \ ref_offset 8b \ size_ref 4b * nb_ref / depth 2b * ( ref_offset[ nb_ref-1 ] - ref_offset[ 0 ] )
29 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes Ref Pos Indi_1 Indi_2 Indi_3 chr chr chr chr chr chr chr chr
30 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes INTERSECT indi_1, indi_2, indi_3 UNION Indi_1, indi_2, indi_
31 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes Gene Indi_1 Indi_2 Indi_3 bar foo foo_bar
32 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes
33 uality reads Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes rname pos indi_1 indi_2 indi_3 At1g_ 586 C: C:T C: GSVIVG A: A: A:T: GSVIVG TC:C C: C: GSVIVG G: G: C:
34 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes paired-end sequences
35 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes paired-end sequences Mapping
36 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes paired-end sequences
37 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes paired-end sequences Mapping Map with expected i_size
38 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes paired-end sequences Mapping Map with expected i_size map with short i_size
39 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes paired-end sequences Mapping Map with expected i_size map with short i_size Right sequence start by soft-clip Left sequence end by soft-clip
40 Mosaik Align. filter coverage and depth Freebayes Pretty Freebayes
41 Carrier et all., in prep
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43 Statistics: 125 cluster users, and 120 Galaxy users (30% IRD, 40% CIRAD, 20% INRA, 10% others) Cluster: jobs / month Client Galaxy: jobs / month, 80 added tools Training courses: 6 training courses organised since 2 years, +150 researchers and students ; Sequence analysis (NGS, comparative genomic, annotation...), and Galaxy usage ; public and private trained people. France, brazil, colombia... ISO 9001 certification in progress: mock audit in september 2012 ; certification audit in december 2012.
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MIRING: Minimum Information for Reporting Immunogenomic NGS Genotyping. Data Standards Hackathon for NGS HACKATHON 1.0 Bethesda, MD September
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