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

被引：131

作者：

Bourgey, Mathieu ^{[1
,2
,3
]}

Dali, Rola ^{[1
,2
,3
]}

Eveleigh, Robert ^{[1
,2
,3
]}

Chen, Kuang Chung ^{[4
,5
]}

Letourneau, Louis ^{[1
,2
,3
]}

Fillon, Joel ^{[6
]}

Michaud, Marc ^{[2
,3
]}

Caron, Maxime ^{[1
,2
,3
,6
]}

Sandoval, Johanna ^{[7
]}

Lefebvre, Francois ^{[1
,2
,3
]}

Leveque, Gary ^{[1
,2
,3
]}

Mercier, Eloi ^{[1
,2
,3
]}

Bujold, David ^{[1
,2
,3
]}

Marquis, Pascale ^{[1
,2
,3
]}

Van, Patrick Tran ^{[8
]}

Morais, David Anderson de Lima ^{[9
]}

Tremblay, Julien ^{[10
]}

Shao, Xiaojian ^{[1
,2
,3
]}

Henrion, Edouard ^{[1
,2
,3
]}

Gonzalez, Emmanuel ^{[1
,2
,3
]}

Quirion, Pierre-Olivier ^{[1
,2
,3
]}

Caron, Bryan ^{[4
,5
]}

Bourque, Guillaume ^{[1
,2
,3
,6
]}

机构：

[1] Canadian Ctr Computat Genom, Montreal, PQ, Canada

[2] McGill Univ, Montreal, PQ, Canada

[3] Genome Quebec Innovat Ctr, Montreal, PQ, Canada

[4] McGill Univ, McGill HPC Ctr, Montreal, PQ, Canada

[5] Calcul Quebec, Montreal, PQ, Canada

[6] McGill Univ, Dept Human Genet, Montreal, PQ, Canada

[7] Beaulieu Saucier Univ Montreal, Pharmacogen Ctr, Montreal, PQ, Canada

[8] Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland

[9] Univ Sherbrooke, CCS, Sherbrooke, PQ, Canada

[10] Natl Res Council Canada, Energy Min & Environm, Montreal, PQ, Canada

来源：

GIGASCIENCE | 2019年 / 8卷 / 06期

基金：

加拿大自然科学与工程研究理事会;

关键词：

genomics; workflow management systems; frameworks; workflow; pipeline; bioinformatics; TOOL; DISCOVERY; PROFILES; ACCURATE; CALLER;

D O I：

10.1093/gigascience/giz037

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Background: 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. Findings: 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. Conclusions: 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.

引用

页数：11

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