Main menu

Efficient de novo assembly of telomere-to-centromere human genomes


50% improvement in NG50 of the nanopore human genome assembly was achieved with current Shasta v0.4 vs. the original Shasta version – from ~20 Mb to ~30 Mb; with ultra-long reads this almost doubled to ~58 Mb.

Human genome assembly time reduced to ~3h with current Guppy basecaller and Shasta v0.4, compared to 6h originally described in their Nature Biotech. publication.

Benedict: “with Shasta and PromethION sequencing, we think that we are achieving efficient, cost-effect, highly contiguous de novo assembly, and making that a practical reality”.

With ultra-long nanopore sequencing, telomere-to-centromere chromosome arm assembly is possible for the majority of chromosome arms.

With their diplotyping pipeline, SNV calling performance ‘was actually better than [on] short-read [data]...which is really exciting’.

Benedict: ‘in regions that are defined as low mappability, we clearly have an advantage’; short-read data maps less well than nanopore data, explaining the poorer SNV calling.

This is the first demonstration that long-read diplotyping can outperform short-read genotyping.

Introducing the Human Pangenome project, Benedict explained: ‘Genomics is failing on diversity – we need to increase the number of complete genomes that we have from a diversity of different human populations, to more fully understand our genetic heritage’.

Authors: Benedict Paten

Getting started

Buy a MinION starter pack Nanopore store Sequencing service providers Channel partners

Nanopore technology

Subscribe to Nanopore updates Resources and publications What is the Nanopore Community

About Oxford Nanopore

News Company timeline Sustainability Leadership team Media resources & contacts For investors For partners Working at Oxford Nanopore Current vacancies Commercial information BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Spanish flag