New Technique Improves Microbial Genome Assembly

Tool simplifies workflow for DNA sample preparation to finished sequence.

Image courtesy of DOE Joint Genome Institute (JGI), Roy Kaltschmidt
DOE JGI researchers have helped develop a technique that uses the Pacific Biosciences sequencing machine to fully automate the workflow for DNA sample preparation, sequencing, and assembly.

The Science

In addition to sequencing the genomes of microbes, plants, fungi, and metagenomes, the Department of Energy’s (DOE) Joint Genome Institute (JGI) develops tools to improve the assembly and analysis of these DNA sequences. One such tool, the hierarchical genome assembly process (HGAP), provides a fully automated workflow for users of Pacific Biosciences’ (PacBio) single-molecule, real-time DNA sequencing machine.

The Impact

HGAP produced final assemblies with >99.999% accuracy when compared to reference sequences for three microbes. With improved sequence assemblies, scientists can more readily use sequencing information to understand the role of biological processes and genes in DOE bioenergy and environmental missions.


The PacBio sequencer generates initial DNA sequences 10 or more times longer than those provided by other technologies, greatly aiding the assembly of sequences into more complete genomes. Competing sequencing technologies involve creating several DNA libraries, conducting multiple sequencing runs, and combining the resulting data. In contrast, HGAP requires just a single, long-insert shotgun DNA library. The approach is able to resolve long regions of repeated DNA sequence that often complicate other assembly methods. This new method was tested using three microbes previously sequenced by DOE JGI. Future work in the project will focus on extending the utility of HGAP beyond microbial genomes to those of larger, more complex organisms.


Jonas Korlach
Pacific Biosciences
Menlo Park, California


The work conducted by the DOE Joint Genome Institute is supported by the Office of Biological and Environmental Research within DOE’s Office of Science.


Chin, C.S., et al. “Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.” Nature Methods 10, 563–569 (2013). [DOI: 10.1038/nmeth.2474]

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