CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.
To install the CircSeqAlignTk package, start R (≥ 4.2) and run the following steps:
if (!require('BiocManager', quietly = TRUE))
install.packages('BiocManager')
BiocManager::install("CircSeqAlignTk")
Vignette, including overview of CircSeqAlignTk package, detailed explanation of functions, and several case studies, can be accesssed with the following steps:
browseVignettes('CircSeqAlignTk')
Sun J, Fu X and Cao W. CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes. F1000Research 2024, 11:1221. doi: 10.12688/f1000research.127348.2.