# CircSeqAlignTk *CircSeqAlignTk* is an end-to-end toolkit for RNA-Seq data analysis of circular genome sequences, supporting tasks from alignment to visualization. It is primarily designed for studying viroids, which are small, circular RNAs typically composed of a few hundred nucleotides. In addition to analysis capabilities, *CircSeqAlignTk* provides a streamlined interface for generating synthetic RNA-Seq data that closely mimics real datasets. This functionality enables developers to benchmark alignment tools, test novel alignment algorithms, and validate new workflows. This vignette offers an overview of *CircSeqAlignTk* and demonstrates its usage. # Installation To install the *CircSeqAlignTk* package, start R (≥ 4.2) and run the following steps: ```{r install_package, eval=FALSE} if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') BiocManager::install('CircSeqAlignTk') ``` Note that to install the latest version of the *CircSeqAlignTk* package, the latest version of R is required. ## Documentation Vignette, including overview of *CircSeqAlignTk* package, detailed explanation of functions, and several case studies, can be accessed with the following code. ``` browseVignettes('CircSeqAlignTk') ``` ## Citation 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](https://doi.org/10.12688/f1000research.127348.2).