RNA-combine – a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms

Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, analysing transcriptome data, or visualizing analysis results. However, most existing tools are limited to data from a single sequencing platform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users, especially those without advanced programming skills. Hence, we still lack an open-source toolkit that enables both bioinformatician and non-bioinformatician users to process and analyze the large transcriptome data from different sequencing platforms and visualize the results.

Researchers from the Chinese Academy of Sciences present a Linux-based toolkit, RNA-combine, to automatically perform the quality assessment, downstream analysis of the transcriptome data generated from different sequencing platforms, including bulk RNA-seq (Illumina platform), single cell RNA-seq (10x Genomics) and Iso-Seq (PacBio) and visualization of the results. Besides, this toolkit is implemented with at least 10 analysis modules more than other toolkits examined in this study.

The Schematic workflow of RNA-combine. It includes three analysis units dealing with bulk RNA-seq, scRNA-seq and Iso-Seq data, respectively

Fig. 1

Availability – Source codes of RNA-combine are available on GitHub: https://github.com/dongxuemin666/RNA-combine.

Dong X, Dong S, Pan S, Zhan X. (2022) RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms. BMC Bioinformatics 23(1):26. [article]

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