Friday, May 10, 2013

DOE JGI Science Highlights: A new technique for microbial genome assembly


A world leader in sequencing microbial genomes (and also sequencing plants, fungi and metagenomes), the DOE Joint Genome Institute is also a national user facility focused on developing tools that more cost-effectively enable the assembly and analysis of the sequence that it generates.
DOE JGI researchers helped develop what is described as 
a fully automated process from DNA sample preparation
to the determination of the finished genome.
(Image credit: Roy Kaltschmidt, LBNL)

One such tool was reported online May 5, 2013 in Nature Methods. Known as HGAP (Hierarchical Genome Assembly Process), the fully automated workflow technique uses Pacific Biosciences' single molecule, real-time DNA sequencing platform, which generates reads that can be up to several thousand bases longer than those provided by the Sanger sequencing technology. 

This de novo assemblymethod was tested using three microbes previously sequenced by the DOE JGI. The data collected were compared against the reference sequences for these microbes and the team found that the HGAP method produced final assemblies with >99.999% accuracy. The Sanger process and later sequencing technologies involved creating multiple DNA libraries, conducting multiple runs, and combining the data. The team said in contrast, HGAP requires just "a single, long-insert shotgun DNA library … prepared and subjected to automated continuous long-read SMRT sequencing, and the assembly is performed without the need for circular consensus sequencing.” Next steps in the project focus on extending the utility of this new assembly method beyond microbes to the genomes of more complex organisms.

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