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Scientists Develop New Cost-Effective Method of Genome Assembly

A collaboration by scientists from the U.S. Department of Energy's Joint Genome Institute (DOE JGI), Pacific Biosciences (PacBio) in California and the University of Washington has led to an improved workflow for genome assembly that the team describes as "a fully automated process from DNA sample preparation to the determination of the finished genome."

A collaboration by scientists from the U.S. Department of Energy's Joint Genome Institute (DOE JGI), Pacific Biosciences (PacBio) in California and the University of Washington has led to an improved workflow for genome assembly that the team describes as "a fully automated process from DNA sample preparation to the determination of the finished genome."

 

The technique, known as HGAP (Hierarchical Genome Assembly Process), uses PacBio's single molecule, real-time DNA sequencing platform, which generates reads that can be up to tens of thousands of nucleotides long, even longer than those provided by the workhorse technology of the Human Genome Project era, the Sanger sequencing technology, which produced reads of about 700 nucleotides. The developers further explained that with HGAP, only a single, long-insert shotgun DNA library is prepared and subjected to automated continuous long-read SMRT sequencing, and the assembly is performed without the need for circular consensus sequencing.

 

View DOE JGI's news release at http://www.jgi.doe.gov/News/news_13_05_06.html.

 

Despite tremendous advances in cost reduction and throughput of DNA sequencing, significant challenges remain in the process of efficiently reconstructing genomes.  Existing technologies are good at cranking out short fragments (reads) of DNA letters that are computationally stitched back together (assembled) into longer pieces, so that the order of those letters can be determined and the function of the target sequence discerned. However, genome assembly, the equivalent of trying to put together a multi-million piece jigsaw puzzle without knowing what the picture on the cover of the box is, remains challenging due to the very large number of very small pieces, which must be assembled using current approaches.

Photo: DOE JGI researchers are part of a team that has developed what is
described as “a fully automated process from DNA sample preparation to the
determination of the finished genome.” (Roy Kaltschmidt, LBNL)

 

 

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