SnakeChunks: modular blocks to build Snakemake workflows for reproducible NGS analyses

Abstract

Abstract Summary Next-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. Availability The code is freely available (github.com/SnakeChunks/SnakeChunks), and documented with tutorials and illustrative demos (snakechunks.readthedocs.io). Contact claire.rioualen@inserm.fr , jacques.van-helden@univ-amu.fr Supplementary information Supplementary data are available at Bioinformatics online.