Role of Galaxy in a bioinformatic plant breeding platform
With NGS development, bioinformatics has become central in plant breeding laboratories, and researchers are in need of some autonomy in its use. The Southgreen platform (CIRAD, IRD, INRA) performs bioinformatics analyses for many plant breeding research teams in Montpellier (France), and offers many systems to users: for example GNPAnnot (automatic genomic sequence annotation), Greenphyl (phylogenetic orthology prediction), ESTtik (EST annotation) or the Bacchus analysis pipeline. Most of these systems have been translated into Galaxy workflows. As for the Bacchus pipeline, it has been created at INRA Montpellier (France) to investigate clonal diversity in grapevine genomes. For this task, many softwares have been wrapped in the Galaxy framework. Bacchus can be decomposed in three steps: i) Genome reconstruction, ii) test of reconstruction results, and iii) diversity analysis. This last step is done using SNP's and structural variations. To detect SNP's, the latest Freebayes version was used, while the IDfixe software was developped for structural variation detection. Some of the softwares developped for this pipeline are now used in the international project Grapereseq. Today, the Galaxy framework is widely used by Southgreen plateform users as an alternative to the command line system. In this context, dozens of users have already been trained in Galaxy-using bioinformatics. During weekly collective pair-programming sessions, platform engineers and interested scientists integrate new tools and functionalities.Thus, Galaxy is now a core component of the plant breeding community around the Southgreen platform, and the main access portal for non- bioinformatics specialists to our computing clusters.
Main Authors: | , , , , , , , , , , , , , , , , , |
---|---|
Format: | conference_item biblioteca |
Language: | eng |
Published: |
s.n.
|
Subjects: | F30 - Génétique et amélioration des plantes, C30 - Documentation et information, U10 - Informatique, mathématiques et statistiques, |
Online Access: | http://agritrop.cirad.fr/568374/ http://agritrop.cirad.fr/568374/1/document_568374.pdf |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cirad-fr-568374 |
---|---|
record_format |
koha |
spelling |
dig-cirad-fr-5683742024-07-03T16:00:41Z http://agritrop.cirad.fr/568374/ http://agritrop.cirad.fr/568374/ Role of Galaxy in a bioinformatic plant breeding platform. Maillol Vincent, Bacilieri Roberto, Bocs Stéphanie, Boursiquot Jean-Michel, Carrier Gregory, Dereeper Alexis, Droc Gaëtan, Fleury Cécile, Larmande Pierre, Le Cunff Loïc, Péros Jean-Pierre, Pitollat Bertrand, Ruiz Manuel, Sarah Gautier, Sempere Guilhem, Summo Marilyne, This Patrice, Dufayard Jean-François. 2012. In : Galaxy Community Conference GCC2012, Chicago, Etats-Unis, July 25-27 2012. s.l. : s.n., Résumé, 1 p. Galaxy Community Conference, Chicago, États-Unis, 25 Juillet 2012/27 Juillet 2012.http://wiki.galaxyproject.org/Events/GCC2012/Abstracts#Role_of_Galaxy_in_a_bioinformatic_plant_breeding_platform <http://wiki.galaxyproject.org/Events/GCC2012/Abstracts#Role_of_Galaxy_in_a_bioinformatic_plant_breeding_platform> Role of Galaxy in a bioinformatic plant breeding platform Maillol, Vincent Bacilieri, Roberto Bocs, Stéphanie Boursiquot, Jean-Michel Carrier, Gregory Dereeper, Alexis Droc, Gaëtan Fleury, Cécile Larmande, Pierre Le Cunff, Loïc Péros, Jean-Pierre Pitollat, Bertrand Ruiz, Manuel Sarah, Gautier Sempere, Guilhem Summo, Marilyne This, Patrice Dufayard, Jean-François eng 2012 s.n. Galaxy Community Conference GCC2012, Chicago, Etats-Unis, July 25-27 2012 F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques With NGS development, bioinformatics has become central in plant breeding laboratories, and researchers are in need of some autonomy in its use. The Southgreen platform (CIRAD, IRD, INRA) performs bioinformatics analyses for many plant breeding research teams in Montpellier (France), and offers many systems to users: for example GNPAnnot (automatic genomic sequence annotation), Greenphyl (phylogenetic orthology prediction), ESTtik (EST annotation) or the Bacchus analysis pipeline. Most of these systems have been translated into Galaxy workflows. As for the Bacchus pipeline, it has been created at INRA Montpellier (France) to investigate clonal diversity in grapevine genomes. For this task, many softwares have been wrapped in the Galaxy framework. Bacchus can be decomposed in three steps: i) Genome reconstruction, ii) test of reconstruction results, and iii) diversity analysis. This last step is done using SNP's and structural variations. To detect SNP's, the latest Freebayes version was used, while the IDfixe software was developped for structural variation detection. Some of the softwares developped for this pipeline are now used in the international project Grapereseq. Today, the Galaxy framework is widely used by Southgreen plateform users as an alternative to the command line system. In this context, dozens of users have already been trained in Galaxy-using bioinformatics. During weekly collective pair-programming sessions, platform engineers and interested scientists integrate new tools and functionalities.Thus, Galaxy is now a core component of the plant breeding community around the Southgreen platform, and the main access portal for non- bioinformatics specialists to our computing clusters. conference_item info:eu-repo/semantics/conferenceObject Conference info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/568374/1/document_568374.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html http://wiki.galaxyproject.org/Events/GCC2012/Abstracts#Role_of_Galaxy_in_a_bioinformatic_plant_breeding_platform info:eu-repo/semantics/altIdentifier/purl/http://wiki.galaxyproject.org/Events/GCC2012/Abstracts#Role_of_Galaxy_in_a_bioinformatic_plant_breeding_platform info:eu-repo/semantics/reference/purl/http://wiki.galaxyproject.org/Documents/Presentations/GCC2012?action=AttachFile&do=view&target=MaillolDufayard.pdf |
institution |
CIRAD FR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cirad-fr |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CIRAD Francia |
language |
eng |
topic |
F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques |
spellingShingle |
F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques Maillol, Vincent Bacilieri, Roberto Bocs, Stéphanie Boursiquot, Jean-Michel Carrier, Gregory Dereeper, Alexis Droc, Gaëtan Fleury, Cécile Larmande, Pierre Le Cunff, Loïc Péros, Jean-Pierre Pitollat, Bertrand Ruiz, Manuel Sarah, Gautier Sempere, Guilhem Summo, Marilyne This, Patrice Dufayard, Jean-François Role of Galaxy in a bioinformatic plant breeding platform |
description |
With NGS development, bioinformatics has become central in plant breeding laboratories, and researchers are in need of some autonomy in its use. The Southgreen platform (CIRAD, IRD, INRA) performs bioinformatics analyses for many plant breeding research teams in Montpellier (France), and offers many systems to users: for example GNPAnnot (automatic genomic sequence annotation), Greenphyl (phylogenetic orthology prediction), ESTtik (EST annotation) or the Bacchus analysis pipeline. Most of these systems have been translated into Galaxy workflows. As for the Bacchus pipeline, it has been created at INRA Montpellier (France) to investigate clonal diversity in grapevine genomes. For this task, many softwares have been wrapped in the Galaxy framework. Bacchus can be decomposed in three steps: i) Genome reconstruction, ii) test of reconstruction results, and iii) diversity analysis. This last step is done using SNP's and structural variations. To detect SNP's, the latest Freebayes version was used, while the IDfixe software was developped for structural variation detection. Some of the softwares developped for this pipeline are now used in the international project Grapereseq. Today, the Galaxy framework is widely used by Southgreen plateform users as an alternative to the command line system. In this context, dozens of users have already been trained in Galaxy-using bioinformatics. During weekly collective pair-programming sessions, platform engineers and interested scientists integrate new tools and functionalities.Thus, Galaxy is now a core component of the plant breeding community around the Southgreen platform, and the main access portal for non- bioinformatics specialists to our computing clusters. |
format |
conference_item |
topic_facet |
F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques |
author |
Maillol, Vincent Bacilieri, Roberto Bocs, Stéphanie Boursiquot, Jean-Michel Carrier, Gregory Dereeper, Alexis Droc, Gaëtan Fleury, Cécile Larmande, Pierre Le Cunff, Loïc Péros, Jean-Pierre Pitollat, Bertrand Ruiz, Manuel Sarah, Gautier Sempere, Guilhem Summo, Marilyne This, Patrice Dufayard, Jean-François |
author_facet |
Maillol, Vincent Bacilieri, Roberto Bocs, Stéphanie Boursiquot, Jean-Michel Carrier, Gregory Dereeper, Alexis Droc, Gaëtan Fleury, Cécile Larmande, Pierre Le Cunff, Loïc Péros, Jean-Pierre Pitollat, Bertrand Ruiz, Manuel Sarah, Gautier Sempere, Guilhem Summo, Marilyne This, Patrice Dufayard, Jean-François |
author_sort |
Maillol, Vincent |
title |
Role of Galaxy in a bioinformatic plant breeding platform |
title_short |
Role of Galaxy in a bioinformatic plant breeding platform |
title_full |
Role of Galaxy in a bioinformatic plant breeding platform |
title_fullStr |
Role of Galaxy in a bioinformatic plant breeding platform |
title_full_unstemmed |
Role of Galaxy in a bioinformatic plant breeding platform |
title_sort |
role of galaxy in a bioinformatic plant breeding platform |
publisher |
s.n. |
url |
http://agritrop.cirad.fr/568374/ http://agritrop.cirad.fr/568374/1/document_568374.pdf |
work_keys_str_mv |
AT maillolvincent roleofgalaxyinabioinformaticplantbreedingplatform AT bacilieriroberto roleofgalaxyinabioinformaticplantbreedingplatform AT bocsstephanie roleofgalaxyinabioinformaticplantbreedingplatform AT boursiquotjeanmichel roleofgalaxyinabioinformaticplantbreedingplatform AT carriergregory roleofgalaxyinabioinformaticplantbreedingplatform AT dereeperalexis roleofgalaxyinabioinformaticplantbreedingplatform AT drocgaetan roleofgalaxyinabioinformaticplantbreedingplatform AT fleurycecile roleofgalaxyinabioinformaticplantbreedingplatform AT larmandepierre roleofgalaxyinabioinformaticplantbreedingplatform AT lecunffloic roleofgalaxyinabioinformaticplantbreedingplatform AT perosjeanpierre roleofgalaxyinabioinformaticplantbreedingplatform AT pitollatbertrand roleofgalaxyinabioinformaticplantbreedingplatform AT ruizmanuel roleofgalaxyinabioinformaticplantbreedingplatform AT sarahgautier roleofgalaxyinabioinformaticplantbreedingplatform AT sempereguilhem roleofgalaxyinabioinformaticplantbreedingplatform AT summomarilyne roleofgalaxyinabioinformaticplantbreedingplatform AT thispatrice roleofgalaxyinabioinformaticplantbreedingplatform AT dufayardjeanfrancois roleofgalaxyinabioinformaticplantbreedingplatform |
_version_ |
1806036954652868608 |