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

Gigascience. 2019 Jun 1;8(6):giz037. doi: 10.1093/gigascience/giz037.

Abstract

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.

Keywords: bioinformatics; frameworks; genomics; pipeline; workflow; workflow management systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Methylation
  • Epigenomics / methods
  • Genomics / methods*
  • Humans
  • Metagenomics / methods
  • Sequence Analysis, DNA / methods
  • Sequence Analysis, RNA / methods
  • Software*

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