Biological samples are subject to variation, and replicates are thus essential to estimate the statistical significance of the final results, and to ensure a tradeoff between sensitivity and specificity. Ideally, the experimental design should already take into account a perspective on the bioinformatics analyses that will enable the extraction of relevant information from the raw data. A workflow, or pipeline, is defined as a chaining of commands and tools applied to a set of data files, so that the output of a given step is used as input for the subsequent one ( Figure 1). The analysis of sequenced reads requires a number of successive bioinformatics processing steps, organized into workflows. Transcription factor binding can be characterized at a genome-scale by ChIP-seq, whereas RNA-seq allows to quantify all the transcripts. Next-generation sequencing technologies enable the characterization of biological gene regulation at an unprecedented scale. They are illustrated by a study combining ChIP-seq and RNA-seq to identify target genes of the global transcription factor FNR in Escherichia coli ( Myers et al., 2013), with the advantage that results can be compared with the most up-to-date collection of existing knowledge about transcriptional regulation in this model organism, extracted from the RegulonDB database ( Gama-Castro et al., 2016). The protocols describe a modular system enabling the user to compose and fine-tune workflows based on SnakeChunks, a library of rules for the Snakemake workflow engine ( KГ¶ster and Rahmann, 2012).

Despite the availability of user-friendly solutions, there is a strong need for accessible solutions to allow experimental biologists to analyze and explore their results in an autonomous and flexible way.

In order to ensure reproducible results, there is a crucial need to improve the automation of processing for the forthcoming studies relying on big datasets.

Next-Generation Sequencing (NGS) is becoming a routine approach for most domains of life sciences.

Conda install package locally