Fast, Cheap, High-Quality Human Genome Assembly Has Arrived
May 14, 2020 | Biotechnology
Reading time: 3 minutes
Fresh from GEN – Genetic Engineering and Biotechnology News, here is a newly released Bio Technology article for you:
Although short read sequencing serves an important purpose in both the research and clinical arenas of genomic analysis, it is difficult to rely on short reads for some interrogations, such as structural variations (SVs) including large indels and base-level resolved copy number variations, to resolve phasing relationships or to generate highly contiguous de novo genome assemblies. For these, long-read sequencing technologies have overcome the limitations of short-reads.
It has been three years since University of California, Santa Cruz (UCSC), researchers proved that long-read human genome assembly can be done, using a nanopore-based technology developed on campus. The method was then improved upon, using the PromethION nanopore sequencer, shortening the time of the genome assembly to about a week.
Now, UCSC researchers have collaborated on an algorithm designed to accurately and precisely assemble individual, complete human genomes from long-read sequencing data in about six hours and for about $70.
The work is published in an article titled, “Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes” in Nature Biotechnology. In the paper, the researchers described how Shasta not only yields comparable or better accuracy as its contemporaries but also has the lowest number of misassemblies.
To enable rapid human genome assembly, the researchers developed Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN.
Shasta is an in-memory computing-driven algorithm that can help complete a de novo human genome assembly in under six hours, the authors said, for an average cost of $70 per sample.
They developed a nanopore long-read sequencing protocol that consistently yields ~60X coverage (~200 gigabases) of a human genome at unprecedented lengths (median read N50 of 42 kb) us... You can read the whole article in the GEN – Genetic Engineering and Biotechnology News Blog.
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