Comprehensive evaluation of RNA-seq alignment methods based on long-read sequencing data

Long-read RNA sequencing (RNA-seq) has revolutionized our ability to comprehensively study transcriptomes, enabling the detection of full-length transcripts. The accurate alignment of long-read RNA-seq is a critical step in downstream analysis. However, with the development of alignment tools and each tool declaring the ability to handle long-read RNA-seq alignment on their own, researchers face the challenge of distinguishing and selecting the most suitable tool for their tasks. But to the best of our knowledge, there is still a lack of comprehensive evaluations on the aligners designed for long-read sequencing data. Here, we conducted a benchmark on five state-of-the-art tools on simulated long-read RNA-seq data from three levels to comprehensively assess the performance of each aligner, and provide valuable insights into the strengths and limitations of each aligner, aiding researchers in selecting the most appropriate tool for their long-read RNA-seq studies. We expected our study to advance the field of transcriptomics and promote the accurate analysis of long-read RNA-seq data in diverse biological contexts.