SPARTA – Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis

SPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. The easy-to-install, complete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping reads to a reference, counting gene features, calculating differential gene expression, and, importantly, checking for potential batch effects within the data set. SPARTA outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots. The workflow is implemented in Python for file management and sequential execution of each analysis step and is available for Mac OS X, Microsoft Windows, and Linux.


To promote the use of SPARTA as a teaching platform, a web-based tutorial is available explaining how RNA-seq data are processed and analyzed by the software.

Availability – Tutorial and workflow can be found at Teaching materials are located at Source code can be downloaded at, implemented in Python and supported on Mac OS X, Linux, and MS Windows.

Contact – Robert B. Abramovitch (

Benjamin K Johnson BK, Matthew B Scholz MB, Tracy K Teal TK, Robert B Abramovitch RB. (2015) SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis. bioRxiv [Epub ahead of print]. [abstract]

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