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Print Print this page now.You have submitted the following abstract to Plant and Animal Genome XXVIII Conference
(January 11- 15, 2020). Receipt of this notice does not guarantee that your submission was complete, free of errors, or accepted for presentation. South Green Resources to Manage Rice Big Genomics Data
Clément Agret , Céline Gottin , Alexis Dereeper , Christine Tranchant-Dubreuil , Annie Chateau , Anne Dievart , Gautier Sarah , Alban Mancheron , Guilhem Sempéré , Manuel Ruiz and Gaëtan Droc , (1)LIRMM, France, (2)CIRAD, UMR AGAP, France, (3)IRD, UMR IPME, Montpellier cedex 5, France, (4)IRD - UMR DIADE, Montpellier, France, (5)INRA, UMR AGAP, France, (6)CIRAD, UMR Intertryp, Montpellier, France, (7)CIRAD, UMR AGAP, Montpellier, France
Abstract Text:
We have developed the Rice Genome Hub, an integrative genome information system that allows centralized access to genomics and genetics data, and analytical tools to facilitate translational and applied research in rice. The hub is built using the Content Management System Drupal with the Tripal module that interacts with the Chado database. The Hub interface provides several functionalities (Blast, DotPlots, Gene Search, JBrowse, Primer Blaster, Primer Designer) to make it easy for querying, visualizing and downloading research data. We also plugged in-house tools developed by the South Green
bioinformatics platform.
Among these tools, Gigwa is a Web-based tool which provides an easy and intuitive way to explore large amounts of genotyping data by filtering the latter based not only on variant features, including functional annotations, but also on genotype patterns.
We also developed RedOak, a reference-free and alignment-free software package that allows for the indexing of a large collection of similar genomes. RedOak can be applied to reads from unassembled genomes, and it provides a nucleotide sequence query function. This software is based on a k-mer approach and has been developed to be heavily parallelized and distributed on several nodes of a cluster. Analysis of presence-absence variation (PAV) of genes among different genomes is a classical output of pan-genomic
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First author
Clément Agret Student
Clement.Agret@lirmm.fr LIRMM
UMR5506 and Université de Montpellier France
Second author Céline Gottin Student
celine.gottin@cirad.fr CIRAD, UMR AGAP
Avenue Agropolis, Montpellier France
IRIC: Rice Informatics for the Global Community Scheduled Date: Wednesday, January 15, 2020 Scheduled Time: 11:10 AM Final Number: W682 Title:
South Green Resources to Manage Rice Big Genomics Data Submitter's E-mail Address:
Third author
Alexis Dereeper Bioinformatician alexis.dereeper@ird.fr IRD, UMR IPME
UMR RPB, Centre IRD Montpellier cedex 5, 34394 France Fourth author Christine Tranchant-Dubreuil Genomic Researcher christine.tranchant@ird.fr IRD - UMR DIADE
601 Avenue d'Agropolis - BP 64501 Montpellier, 34394 France Fifth author Annie Chateau Bioinformatician Annie.Chateau@lirmm.fr LIRMM
Sixth author Anne Dievart
Genetic Researcher anne.dievart@cirad.fr CIRAD, UMR AGAP Avenue Agropolis France Seventh author Gautier Sarah Bioinformatician gautier.sarah@inra.fr INRA, UMR AGAP Avenue Agropolis France Eighth author Alban Mancheron Bioinformatician alban.mancheron@lirmm.fr LIRMM
UMR5506 and Université de Montpellier France
Ninth author
Guilhem Sempéré Computer scientist
guilhem.sempere@cirad.fr CIRAD, UMR Intertryp Baillarguet
Montpellier, 34394 France
Tenth Presenting Author Presenting Author
Manuel Ruiz Bioinformatician manuel.ruiz@cirad.fr CIRAD, UMR AGAP Avenue Agropolis Montpellier, 34398 France Eleventh author Gaëtan Droc Bioinformatician gaetan.droc@cirad.fr CIRAD, UMR AGAP Avenue agropolis
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