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A new cost-effective genome assembly process
Date:5/5/2013

e data, so that gaps in the code were covered and accuracies of a DNA base assignment were very high. Post-Sanger methods still typically require multiple libraries and often a mix of technologies to produce optimal results. Instead, 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, the team reported.

This de novo assembly method 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.

We are always on the lookout for new approaches that will improve upon the efficient delivery of high-quality data to our growing community of researchers, said Len Pennacchio, DOE JGIs Deputy Director of Genomic Technologies. This technique is one of many improvements that we are pursuing in parallel to achieve additional economies of scale.

The DOE JGIs sequencing efforts account for more than 20% of the more than 20,000 worldwide genome projects (microbes, plants, fungi, algae, and communities of microbes) completed or currently in the queue, and most of those are focused on the biology of environmental, energy, and carbon processing.

We enjoyed a very productive collaboration with JGI on this project and benefitted tremendously from the expertise of JGIs scientists in both the fields of microbiology and microbial genome assembly and annotation, said Jonas Korlach, Chief Scientific Officer at Pacific Biosciences. This expertise provided us with the ability to adapt our single molecule sequencing assembly methods to produce a higher level of finished quality than was previously possible using a gold-standard Sanger finishing approach, and at a speed and price point competitive with alternative next generation s
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Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert

Page: 1 2 3

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