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bioRxiv · 10.1101/165191

SnakeChunks: modular blocks to build Snakemakeworkflows for reproducible NGS analyses

Rioualen, C.·Charbonnier-Khamvongsa, L.·van Helden, J.
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Abstract

SummaryNext-Generation Sequencing (NGS) is becoming a routine approach for most domains of life sciences, yet there is a crucial need to improve the automation of processing for the huge amounts of data generated and to ensure reproducible results. We present SnakeChunks, a collection of Snakemake rules enabling to compose modular and user-configurable workflows, and show its usage with analyses of transcriptome (RNA-seq) and genome-wide location (ChIP-seq) data.\n\nAvailabilityThe code is freely available (github.com/SnakeChunks/SnakeChunks), and documented with tutorials and illustrative demos (snakechunks.readthedocs.io).\n\nContactclaire.rioualen@inserm.fr, jacques.van-helden@univ-amu.fr\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

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Rioualen, C., Charbonnier-Khamvongsa, L., van Helden, J.. 2017-07-19. SnakeChunks: modular blocks to build Snakemakeworkflows for reproducible NGS analyses. https://doi.org/10.1101/165191

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