Bioinformatic pipeline for analysing variations in long-reads reconstructed human genomes v1

Recent advances in sequencing technologies have paved the way for personalized medicine and clinical genomics, providing unprecedented insights into the genetic basis of human health and disease. High-throughput sequencing is now recognized as an effective diagnostic tool for patients affected by rare diseases but the use of either Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) technologies has shown to be uninformative in many cases. On the contrary, the recent introduction of long-read technologies can resolve genomic regions inaccessible to short-read sequencing, but a reliable benchmark assessment is missing. Following a long and intense benchmarking activity, here we present our bioinformatic pipeline based on Oxford Nanopore Technology (ONT) long reads aimed at shading lights to the stages of alignment, SNVs, indels, and SV calling, and modified bases analysis.