Skip to main content
eScholarship
Open Access Publications from the University of California

High Quality Microbial Finishing at JGI

Abstract

The value of complete microbial genome sequence is established and appreciated by scientific community. A finished genome represents the genome assembly of high accuracy and quality (with no gaps), verified and confirmed through a number of computer and lab experiments. Several yeas ago JGI has established a set of high standards for the final microbial assembly and has been strictly following them thereafter. More than 100 microbial projects have been completed since that time within the framework of the JGI s portfolio (DOE GTL program, DOE Microbial program and the Community Sequencing Program). Progress in DNA sequencing technology, design of new vectors for library construction, improvements in finishing strategies and tools, as well as the availability of a number of assemblers and advanced methods for OFR finding and genome annotation have significantly reduced the time required for genome closure. Despite this fact, complexity and speed of genome closure depends on the quality of DNA received, the whole genome shotgun libraries produced from this DNA, GC content of the genome, the size and frequency of identical or nearly identical repetitive structures, and the amount of regions that can not be cloned or hard to clone in E.coli. The whole genome finishing/assembly improvement pipeline will be presented showing the lab approaches and computational finishing techniques developed and implemented at JGI for finishing the large number of microbial projects in the queue. We also will present our progress in completing metagenomic projects. A number of projects for which the combination of different sequencing technologies (Sanger and 454) and finishing strategies were used will also be presented.

Main Content
For improved accessibility of PDF content, download the file to your device.
Current View