Variant Detection with HiFi Reads - Understanding Results from the precisionFDA Truth Challenge
In this short video, Aaron Wenger, a Principal Scientist at PacBio, explains what highly accurate long reads, or HiFi reads, are and how they help to detect all variant types including single nucleotide, indels, and structural variants. He goes on to recap the precisionFDA Truth Challenge V2 which used Genome in a Bottle (GIAB) benchmarks to evaluate various sequencing technologies. In the 2020 challenge, when ranked for accuracy, PacBio HiFi reads delivered the highest precision and recall in all categories.
0:00 Introduction
0:11 VARIANT = DIFFERENCE BETWEEN AN INDIVIDUAL AND THE REFERENCE GENOME
0:51 HIFI READS ARE LONG (15-20 KB) AND ACCURATE (99%)
2:45 HIFI READS SPAN STRUCTURAL VARIANTS 1,733 bp deletion
3:12 MEASURING PERFORMANCE WITH GENOME IN A BOTTLE BENCHMARKS, HG001-HG007
4:22 GENOME IN A BOTTLE V3.3.2 BENCHMARKS (2017) SHORT AND LINKED READS
4:48 GENOME IN A BOTTLE V4 BENCHMARKS (2020) SHORT, LINKED, AND HIFI READS
5:18 PRECISION FDA TRUTH CHALLENGE V2
7:37 PATHOGENIC VARIANTS DETECTED WITH PACBIO
Learn more about HiFi Sequencing at https://pacb.com/HiFi
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