Long-read direct RNA sequencing of the GIAB HG002, HG004, and HG005 using Oxford Nanopore Technologies with SQK-RNA004 kit

Data released for Clair3-RNA, A long-read small variant caller for RNA sequencing data. Variant calling using long-read RNA sequencing (lrRNA-seq) can be applied to diverse tasks, such as capturing full-length isoforms and gene expression profiling. It poses challenges, however, due to higher error rates than DNA data, the complexities of transcript diversity, RNA editing events, etc. In this paper, we propose Clair3-RNA, a deep learning-based variant caller tailored for lrRNA-seq data. Clair3-RNA leverages the strengths of the Clair series pipelines and incorporates several techniques optimized for lrRNA-seq data, such as uneven coverage normalization, refinement of training materials, and editing site discovery, to enhance variant-calling performance. Clair3-RNA is available for various platforms, including PacBio and ONT complementary DNA sequencing (cDNA), and ONT direct RNA sequencing (dRNA). Clair3-RNA is open-source and available at (https://github.com/HKU-BAL/Clair3-RNA).