van Helden, J. | Search bioRxiv

bioRxiv2017

SnakeChunks: modular blocks to build Snakemakeworkflows for reproducible NGS analyses

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.

bioinformatics↗

bioRxiv2017

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

SummaryWe designed a PyQt graphical user interface - Sequanix - aiming at democratizing the use of Snakemake pipelines. Although the primary goal of Sequanix was to facilitate the execution of NGS Snakemake pipelines available in the Sequana project (http://sequana.readthedocs.io), it can also handle any Snakemake pipelines. Therefore, Sequanix should be useful to all Snakemake developers willing to expose their pipelines to a wider audience.\n\nAvailabilitySource code available on http://github.com/sequana/sequana and standalone on http://bioconda.github.io (sequana package).

bioinformatics↗