SUMMER: an integrated nanopore sequencing pipeline for variants detection and clinical annotation on the human genome

• DOI: 10.1007/s10142-025-01534-z
• Publication Date: 2025-01-21T06:34:58Z
• Authors: Renqiuguo Li; Hongyuan Chu; Kai Gao; Huaxia Luo; Yuwu Jiang
• Keywords: Nanopore

Long-read sequencing has emerged as a transformative technology in recent years, offering significant potential for the molecular diagnosis of unresolved genetic disorders. Despite its promise, comprehensive detection and clinical annotation genomic variants remain intricate technically demanding. We present SUMMER, an integrated structured workflow specifically designed to process raw Nanopore reads. SUMMER facilitates in-depth analysis multiple variant types, including SNV, SV, short tandem repeat mobile element insertion. For applications, employs SvAnna prioritize SV candidates based on phenotype relevance utilizes Straglr provide reference distributions non-pathogenic unit counts 55 known pathogenic repeats. By addressing critical challenges annotation, seeks advance utility long-read diagnostic genomics. is available web at https://github.com/carolhuaxia/summer .