What it is
Researchers built a telomere-to-telomere benchmark for the diploid HG002 genome that reaches near-perfect accuracy, with no detectable errors, across 99.4% of the complete sequence. It adds 701.4 Mb of autosomal sequence plus 216.8 Mb of both sex chromosomes, covering 15.3% of the genome that prior benchmarks omitted, and includes a diploid annotation of 39,144 protein-coding genes across both haplotypes. Using the benchmark's own accuracy tools, de novo assembly resolved 2-7% more sequence than read mapping and made just one error per 100 kb across 99.9% of benchmark regions.
Why it matters
Standard resequencing maps reads to a reference and inherits its biases, so duplicated and structurally polymorphic regions go uncalled and the benchmarks built the same way cannot even measure accuracy there. A complete diploid truth set covering the 15.3% of the genome that was previously unassessable lets methods be scored where they actually fail, and it shows assembly-based approaches beating variant calling by an order of magnitude.
Underlined numbers link to their source. Every metric and quoted figure is listed under Sources and data below.
Filed undergenomics, telomere-to-telomere, benchmark, diploid-genome, personalized-medicine