Sindbis virus strain:Toto 1101 Raw sequence reads

The current project utilized Oxford Nanopore Technologies Direct RNA Sequencing to detect potential modified A sites in the native viral RNA molecules. Viral RNAs were obtained from SINV-infected mammalian BHK-21 and mosquito C6/36 cells, and in vitro-transcribed RNA was prepared as a standard negative control. Ten computational tools, including three single-mode methods and seven comparative methods, were applied for modification detection. Their performance was comprehensively evaluated and compared, and an integrated pipeline was proposed accordingly. In conclusion, our project underscores the need for careful application of computational tools in the analysis of viral epitranscriptomics. It also offers insights into alphaviral RNA modifications through a rigorous yet sensitive pipeline.