Titre
GenPipes: an open-source framework for distributed and scalable genomic analyses.
Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
Auteur(s)
Bourgey, M.
Auteure/Auteur
Dali, R.
Auteure/Auteur
Eveleigh, R.
Auteure/Auteur
Chen, K.C.
Auteure/Auteur
Letourneau, L.
Auteure/Auteur
Fillon, J.
Auteure/Auteur
Michaud, M.
Auteure/Auteur
Caron, M.
Auteure/Auteur
Sandoval, J.
Auteure/Auteur
Lefebvre, F.
Auteure/Auteur
Leveque, G.
Auteure/Auteur
Mercier, E.
Auteure/Auteur
Bujold, D.
Auteure/Auteur
Marquis, P.
Auteure/Auteur
Van, P.T.
Auteure/Auteur
Anderson de Lima Morais, D.
Auteure/Auteur
Tremblay, J.
Auteure/Auteur
Shao, X.
Auteure/Auteur
Henrion, E.
Auteure/Auteur
Gonzalez, E.
Auteure/Auteur
Quirion, P.O.
Auteure/Auteur
Caron, B.
Auteure/Auteur
Bourque, G.
Auteure/Auteur
Liens vers les unités
ISSN
2047-217X
Statut éditorial
Publié
Date de publication
2019-06-01
Volume
8
Numéro
6
Peer-reviewed
Oui
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: ppublish
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.
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.
PID Serval
serval:BIB_52A465B393FA
PMID
Open Access
Oui
Date de création
2019-06-24T06:11:03.877Z
Date de création dans IRIS
2025-05-20T19:28:27Z
Fichier(s)![Vignette d'image]()
En cours de chargement...
Nom
31185495_BIB_52A465B393FA.pdf
Version du manuscrit
preprint
Licence
https://creativecommons.org/licenses/by/4.0
Taille
17.84 MB
Format
Adobe PDF
PID Serval
serval:BIB_52A465B393FA.P001
URN
urn:nbn:ch:serval-BIB_52A465B393FA9
Somme de contrôle
(MD5):6aa701d60c84ec7c74e5f010561b37ec