Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Abstract

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.

Genome graphs and the evolution of genome inference

“…Over a number of years, the genome assembly has steadily improved (International Human Genome Sequencing Consortium 2004; Church et al 2011) to the point that the current Genome Reference Consortium (GRC) human genome assembly, GRCh38 (Schneider et al 2017), is arguably the best assembled mammalian genome in existence, with just 875 remaining assembly gaps and fewer than 160 million unspecified "N" nucleotides (as of GRCh38.p8).…”

“…5). These graphs were then used to generate linear reference sequences for the two arrays (Miga et al 2014), using a Markovian traversal, and have subsequently been used to define linear representations of the centromeres that are included in GRCh38 (Schneider et al 2017). …”

“…The current human genome assembly, GRCh38 (Schneider et al 2017), contains alternative loci that provide different versions of sequences already represented in the primary assembly (see the section "Richer reference structures"). Mappers which can make sense of these additional representations, either as special linear sequences or as components of a graph, are marked as "alt-aware" in Table 2.…”

The Juicebox Assembly Tools module facilitatesde novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000

“…Scaffolds can contain errors in contig order (a 'translocation') or orientation (an 'inversion'). Examples of such errors can be found in the best available reference genomes for many species (Robert B. Norgren 2013;Shearer et al 2014;Tang et al 2014;Chen et al 2015;Davey et al 2016;Utsunomiya et al 2016;Schneider et al 2017;Korlach et al 2017). Consequently, inexpensive methods for identifying and correcting assembly errors are crucial for the generation of accurate assemblies (Salzberg and Yorke 2005;Phillippy, Schatz, and Pop 2008;Gnerre et al 2009;Tsai, Otto, and Berriman 2010;Salzberg et al 2012;Hunt et al 2013;Gurevich et al 2013;Bradnam et al 2013;Simão et al 2015;Fierst 2015;Muggli et al 2015;Yuan et al 2017;Harewood et al 2017).…”

New advances in sequence assembly

“…This issue marks the 38th build of the human reference sequence (Schneider et al 2017), which still contains more than 800 gaps after decades of work and billions of dollars spent. But there is hope on the horizon.…”