ASHG CoLab: PacBio HiFi reads for comprehensive characterization of genomes and single-cell isoform expression

In this ASHG 2020 CoLab presentation hear Principal Scientists, Aaron Wenger and Elizabeth Tseng share how highly accurate long reads (HiFi reads) provide comprehensive variant detection for both genomes and transcriptomes. Aaron Wenger describes how new improvements in protocols and analysis methods have increased scalability and accuracy of variant calling. As demonstrated in the precisionFDA Truth Challenge V2, HiFi reads (>99% accurate, 15 kb – 20 kb) now outperform short reads for single nucleotide and structural variant calling and match for small indels. This includes calling >30,000 small variants and >10,000 structural variants missed by short reads, many in medically relevant genes. Elizabeth Tseng descried how for Single-Cell RNA sequencing, HiFi reads allow for precise detection of UMIs and single cell barcodes while still providing full-length transcript isoform information. Any single cell platform that produces full-length cDNA can be sequenced on the PacBio Systems, with the Sequel II System generating up to 3 million full-length reads per SMRT Cell 8M, sufficient to characterize ~3,000 single cells.