Yan-Lam Lee
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View article: Clair3-RNA: a deep learning-based small variant caller for long-read RNA sequencing data
Clair3-RNA: a deep learning-based small variant caller for long-read RNA sequencing data Open
Variant calling with long-read RNA sequencing (lrRNA-seq) helps to analyze full-length isoforms and gene expression but is complicated by high error rates, transcript diversity, RNA editing events, etc. Here, we propose Clair3-RNA, the fir…
View article: ClairS-TO: A deep-learning method for long-read tumor-only somatic small variant calling
ClairS-TO: A deep-learning method for long-read tumor-only somatic small variant calling Open
Accurate identification of somatic variants in tumor is crucial but challenging, and typically requires a matched normal sample for reliable detection, which is often unavailable in real-world research and clinical scenarios, necessitating…
View article: Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data
Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data Open
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 co…
View article: ClairS: a deep-learning method for long-read somatic small variant calling
ClairS: a deep-learning method for long-read somatic small variant calling Open
Identifying somatic variants in tumor samples is a crucial task, which is often performed using statistical methods and heuristic filters applied to short-read data. However, with the increasing demand for long-read somatic variant calling…
View article: Evaluation of<i>Mycobacterium Tuberculosis</i>enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling
Evaluation of<i>Mycobacterium Tuberculosis</i>enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling Open
Sensitive detection of Mycobacterium Tuberculosis (TB) in small percentages in metagenomic samples is essential for microbial classification and drug resistance prediction, and assisting in diagnosis and treatment planning. However, tradit…