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ProkSeq for complete analysis of RNA-Seq data from prokaryotes

2020; Oxford University Press; Volume: 37; Issue: 1 Linguagem: Inglês

10.1093/bioinformatics/btaa1063

1367-4811

A. K. M. Firoj Mahmud, Nicolas Delhomme, Soumyadeep Nandi, Maria Fällman,

Molecular Biology Techniques and Applications

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.ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container https://hub.docker.com/repository/docker/snandids/prokseq-v2.0, or can be used through Anaconda: https://anaconda.org/snandiDS/prokseq. The code is available on Github: https://github.com/snandiDS/prokseq and a detailed user documentation, including a manual and tutorial can be found at https://prokseqV20.readthedocs.io.Supplementary data are available at Bioinformatics online.