ProkSeq for complete analysis of RNA-seq data from prokaryotes

SummarySince 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, the current tools for assessing gene expression have been designed around the structures of eukaryotic genes. There are a few stand-alone tools designed for prokaryotes, and they require improvement. A well-defined pipeline for prokaryotes that includes all the necessary tools for quality control, 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, and it produces publication-quality figures. Availability and implementationProkSeq is implemented in Python and is published under the ISC open source license. The tool and a detailed user manual are hosted at Docker: https://hub.docker.com/repository/docker/snandids/prokseq-v2.1, Anaconda: https://anaconda.org/snandiDS/prokseq; Github: https://github.com/snandiDS/prokseq.