CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes

Abstract

RNA sequencing (RNA-seq) technology has now become one of the standard tools for studying biological mechanisms at the transcriptome level. Advances in RNA-seq technology have led to the emergence of a large number of publicly available tools for RNA-seq data analysis. Most of them target linear genome sequences although it is necessary to study organisms with circular genome sequences. For example, by studying the infection mechanisms of viroids which comprise 246–401 nucleotides circular RNAs and target plants, tremendous economic and agricultural damage may be prevented. Unfortunately, using the available tools to construct workflows for the analysis of circular genome sequences is difficult, especially for non-bioinformaticians. To overcome this limitation, we present CircSeqAlignTk, an easy-to-use and richly documented R package. CircSeqAlignTk performs end-to-end RNA-seq data analysis, from alignment to the visualization of circular genome sequences, through a series of functions. Additionally, it implements a function to generate synthetic sequencing data that mimics real RNA-seq data obtained from biological experiments. CircSeqAlignTk not only provides an easy-to-use analysis interface for novice users but also allows developers to evaluate the performance of alignment tools and new workflows.

Predicting symptom severity in PSTVd‐infected tomato plants using the PSTVd genome sequence

“…The sequenced reads of the seven PSTVd isolates were pre‐processed using flexbar v. 3.5.0 (Roehr et al., 2017 ) for trimming adapter sequences. Only reads with lengths between 21 and 24 nt were mapped onto the genomic RNAs of the PSTVd isolates using CircSeqAlignTk (Sun et al., 2022 ) to summarize the expression profiles of vd‐sRNAs.…”