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: http://bit.ly/JGI-Assembly.

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-23.2 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

May 10, 2019
Quantifying Decision Uncertainty in Water Management via a Coupled Agent-Based Model
Considering risk perception can improve the representation of human decision-making processes in age [more...]

May 09, 2019
Projecting Global Urban Area Growth Through 2100 Based on Historical Time Series Data and Future Scenarios
Study provides country-specific urban area growth models and the first dataset on country-level urba [more...]

May 05, 2019
Calibrating Building Energy Demand Models to Refine Long-Term Energy Planning
A new, flexible calibration approach improved model accuracy in capturing year-to-year changes in bu [more...]

May 03, 2019
Calibration and Uncertainty Analysis of Demeter for Better Downscaling of Global Land Use and Land Cover Projections
Researchers improved the Demeter model’s performance by calibrating key parameters and establi [more...]

Apr 22, 2019
Representation of U.S. Warm Temperature Extremes in Global Climate Model Ensembles
Representation of warm temperature events varies considerably among global climate models, which has [more...]

List all highlights (possible long download time)