BER launches Environmental System Science Program. Visit our new website under construction!

U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

New Technique for Improved Microbial Genome Assembly
Published: May 05, 2013
Posted: June 20, 2013

In addition to sequencing the genomes of microbes, plants, fungi, and metagenomes, the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI) develops tools to improve the assembly and analysis of the DNA sequences that it generates. One tool, HGAP (Hierarchical Genome Assembly Process), provides a fully automated workflow for users of the Pacific Biosciences’ single molecule, real-time DNA sequencing machine. The “PacBio” sequencer generates initial DNA sequences up to 10 or more times longer than those provided by other technologies, which is a great assistance in the assembly of sequences into more complete genomes, but at a higher cost and lower accuracy. Competing sequencing technologies involve creating multiple DNA libraries, conducting multiple runs, and combining the data. I n contrast, HGAP requires just a single, long-insert, shotgun DNA library, enabling the resolution of long regions of repeated DNA sequence that often complicate other assembly methods. This new assembly method was tested using three microbes previously sequenced by DOE JGI. The HGAP produced final assemblies with >99.999% accuracy when compared to the reference sequences for these microbes. Next steps in the project will focus on extending HGAP’s utility beyond microbes to the larger genomes of more complex organisms. By improving sequence assemblies in this way, sequencing information can more readily be developed into understanding the role of biological processes and genes in DOE bioenergy and environmental missions.

Reference: Chin, C.-S., D. H. Alexander, P. Marks, A. K. Klammer, J. Drake, C. Heiner, A. Clum, A. Copeland, J. Huddleston, E. E. Eichler, S. W. Turner, and J. Korlach. 2013. “Nonhybrid, Finished Microbial Genome Assemblies from Long-Read SMRT Sequencing Data,” Nature Methods 10, 563–69. DOI: 10.1038/nmeth.2474. (Reference link)

For more information, see:

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: DOE Joint Genome Institute (JGI)

Division: SC-33.2 Biological Systems Science Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Mar 23, 2021
Molecular Connections from Plants to Fungi to Ants
Lipids transfer energy and serve as an inter-kingdom communication tool in leaf-cutter ants&rsqu [more...]

Mar 19, 2021
Microbes Use Ancient Metabolism to Cycle Phosphorus
Microbial cycling of phosphorus through reduction-oxidation reactions is older and more widespre [more...]

Feb 22, 2021
Warming Soil Means Stronger Microbe Networks
Soil warming leads to more complex, larger, and more connected networks of microbes in those soi [more...]

Jan 27, 2021
Labeling the Thale Cress Metabolites
New data pipeline identifies metabolites following heavy isotope labeling.

Analysis [more...]

Aug 31, 2020
Novel Bacterial Clade Reveals Origin of Form I Rubisco

  • All plant biomass is sourced from the carbon-fixing enzyme Rub [more...]

List all highlights (possible long download time)