GenPipes: an open-source framework for distributed and scalable genomic analyses.
Détails
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Etat: Public
Version: de l'auteur⸱e
Licence: CC BY 4.0
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
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
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.
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