# CircSeqAlignTk
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.
## Installation
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")
```
## Documentation
Vignette, including overview of CircSeqAlignTk package,
detailed explanation of functions, and several case studies,
can be accesssed with the following steps:
```
browseVignettes('CircSeqAlignTk')
```
## Reference
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).
