Structural & Functional Annotation Information System (DB)

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Presentation transcript:

Structural & Functional Annotation Information System (DB) Combining : Genetics, Genomics, Transcriptomics, Epigenetics & Agronomy New Varieties Candidate Genes Data Mining Gene Families Phylogeny Comparative Genomics Genome Evolution Paleogenomics Pathways Cis-Regulatory Element QTLs Pseudo- molecules Sequencing Assembling Contigs Scaffolds Physical Map Genetic Maps BAC Contigs Agronomic Traits BACs Anchoring Markers Biotic & Abiotic stresses Structural & Functional Annotation Artemis GenomeView Apollo Information System (DB) Manual curation Pipeline

Annotation Annotation is one of the most difficult tasks in genome sequencing projects, yet it is essential for connecting genome sequence to biology Elsik et al. 2006 Genome Research

TriAnnot Architecture – v5.3p01

Parallelization – short workflow RepeatMasker Mask TEs ClariTE Augustus FGeneSH BLASTn / Exonerate - RNAseq BLASTn / Exonerate - Dong BLASTn / Exonerate - FLcDNA BLASTn / Exonerate - ESTs BLASTx / Exonerate - ATAprp BLASTx / Exonerate - TURprp BLASTx / Exonerate - HORDprp BLASTx / Exonerate - BRACprp BLASTx / Exonerate - ORYZprp BLASTx / Exonerate - SORGprp BLASTx / Exonerate - ZEAMprp BLASTx / Exonerate - RefProtMethForWheatPipe SIMsearch CAT01 SIMsearch CAT02 MERGE ProteinMaker FuncAnnot InterProScan Sequence Prot1 Prot2 Prot3 Prot4 Prot5 Prot6 Protn

Parallelization – short workflow First round Second round Third round Seq 1 Seq 2 Seq 3 Seq N

Parallelization – short workflow Split sequence Seq 1 Seq 1_ Chunk1 Seq 1_ Chunk2 Seq 1_ Chunk3 Seq 1_ Chunk4 Seq 2 Seq 2_ Chunk1 Seq 2_ Chunk2 Seq 2_ Chunk3 Seq 2_ Chunk4

Frédéric GAUDET LIMOS - UCA VM TriAnnot cluster mode TriAnnot deployments - PRABI-AMSB, Lyon - PRABI-Doua, Lyon - PRABI-Gerland, Lyon - PrabiG, Grenoble - PRABI-Lyon Sud - INCa-SLC Frédéric GAUDET LIMOS - UCA VM TriAnnot cluster mode David GRIMBICHLER GenoToul

Objectives Finalize v5.3 Alternative splicing 5’ & 3’ UTR Augustus/Hints YAST  SNPs Alternative splicing 5’ & 3’ UTR Databanks update Share the code with the international community through a software forge (open license) Update documentation (DokuWiki) https://sourcesup.renater.fr/wiki/triannot Update WEB pages https://www.clermont.inra.fr/triannot VM TriAnnot LIMOS – Frédéric Gaudet

TriAnnot Cloud Ability to use Cloud Compute Resource Stick with Slurm execution backend Create Image which could be easily duplicated Build cluster from a ‘playbook’ Launch on every (openstack) Cloud

Databases already there, offering NFS exports

All TriAnnot clients mount databases and share home directory

Main Advantages No wait Environnement is under control Reproductible builds

Acknowledgements Dev Admin Collaborateurs anciens P. Leroy H. Rimbert P. Dufour L. Cerutti B. Laubin F. Sabot F. Legeai E. Gicquelo F. Giacomoni C. Caron I. Blanc-Lenfle A. Mahul A. Claude M. Liauzu T. Flutre I. Luyten C. Pelegrin O. Inizan M. Reichstadt S. Reboux N. Amano H. Numa T. Tanaka M. Seidel K. Mayer H. Ohyanagi S. Theil C. Feuillet H. Sakai T. Itoh H. Quesneville C. Vernette F. Pillot R. Pelegrin L. Subra Bernard A-A Josselin P. Leroy H. Rimbert N. Guilhot M. Alaux C. Viseux M. Loaec F. Alfama-Depauw F. Gaudet Funding from the European Community's FP7 Programme - GA FP7-212019 L. Sterck A. Mahul D. Grimbichler