Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results.

Availability and implementation

ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container, or can be used through Anaconda: The code is available on Github: and a detailed user documentation, including a manual and tutorial can be found at

Supplementary information

Supplementary data are available at Bioinformatics online.

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