2. 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

3. 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 Genome Research

4. TriAnnot Architecture – v5.3p01

5. 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

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

7. 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

8. 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

9. 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)
Update WEB pages
VM TriAnnot
LIMOS – Frédéric Gaudet

10. 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

11. Databases already there, offering NFS exports

12. All TriAnnot clients mount databases and share home directory

13. Main Advantages No wait Environnement is under control
Reproductible builds

14. 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 FP
L. Sterck
A. Mahul
D. Grimbichler