Brief thoughts on Karyn Meltz Steinberg's ASHG 2015 talk on genome assembly improvement

I like it when people a) share their slides online and b) share their slides online soon after they give a talk somewhere. This is particularly helpful when want to quickly catch up on developments from a conference that you couldn't attend. Karyn Meltz Sternberg (@KMS_Meltzy on twitter) ticks both boxes because she posted her #ASHG2015 slides almost as soon as her talk finished. The title of her talk was:

Building a platinum human genome assembly from single haplotype human genomes generated from long molecule sequencing

Her slides — hosted on Slideshare — are embedded below.

What interested me from this talk is the use of sequence maps generated by the BioNano Genomics Irys platform to improve genome assemblies. This technology seems to be growing in popularity, offering an easier (and more powerful?) alternative to 'traditional' optical map solutions. This work is part of the McDonnell Genome Institute's Reference Genomes Improvement project, which includes the following — very laudable — aim:

  • We plan to identify and resolve issues (misassemblies, sequence errors, and gaps) within the current reference GRCh38.

I find it interesting that this project has also defined two levels of genome status:

Gold Genome: A high-quality, highly contiguous representation of the genome with haplotype resolution of critical regions.

Platinum Genome: A contiguous, haplotype-resolved representation of the entire genome.

Not clear from these definitions whether platinum genomes can still include short regions of unknown bases (Ns). A figure on the Reference Genomes Improvement project page also hints at a 'Silver' status, making me think it it only a matter of time before we see the addition of a credit-card-esque 'diamond' status level: no unknown bases, with full representation of tandem repeat arrays, e.g. centromeres, and priority booking for VIP tickets at major sporting events.