GenPipes: an open-source framework for distributed and scalable genomic analyses.

Détails

Ressource 1Télécharger: 31185495_BIB_52A465B393FA.pdf (18266.91 [Ko])
Etat: Public
Version: de l'auteur⸱e
Licence: CC BY 4.0
ID Serval
serval:BIB_52A465B393FA
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
GenPipes: an open-source framework for distributed and scalable genomic analyses.
Périodique
GigaScience
Auteur⸱e⸱s
Bourgey M., Dali R., Eveleigh R., Chen K.C., Letourneau L., Fillon J., Michaud M., Caron M., Sandoval J., Lefebvre F., Leveque G., Mercier E., Bujold D., Marquis P., Van P.T., Anderson de Lima Morais D., Tremblay J., Shao X., Henrion E., Gonzalez E., Quirion P.O., Caron B., Bourque G.
ISSN
2047-217X (Electronic)
ISSN-L
2047-217X
Statut éditorial
Publié
Date de publication
01/06/2019
Peer-reviewed
Oui
Volume
8
Numéro
6
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: ppublish
Résumé
With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing.
Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences long-read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has already been configured on several servers, and a Docker image is also available to facilitate additional installations.
GenPipes offers genomics researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
Mots-clé
bioinformatics, frameworks, genomics, pipeline, workflow, workflow management systems
Pubmed
Open Access
Oui
Création de la notice
24/06/2019 7:11
Dernière modification de la notice
30/04/2021 6:10
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