This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: This work was supported by grants from the Natural Sciences & Engineering Research Council (NSERC) of Canada ( ) and the Canada Research Chairs Program ( ) to DSG. Received: AugAccepted: OctoPublished: November 2, 2011Ĭopyright: © 2011 O'Brien et al.
The rapid and low-cost generation of large numbers of enhanced-quality draft genome sequences will be of particular value for microbial diagnostics and biosecurity, which rely on precise discrimination of potentially dangerous clones from closely related benign strains.Ĭitation: O'Brien HE, Gong Y, Fung P, Wang PW, Guttman DS (2011) Use of Low-Coverage, Large-Insert, Short-Read Data for Rapid and Accurate Generation of Enhanced-Quality Draft Pseudomonas Genome Sequences. We use a combination of Illumina paired-end and mate-pair sequencing, and surprisingly find that de novo assemblies with 100x paired-end coverage and mate-pair sequencing with as low as low as 2–5x coverage are substantially better than assemblies based on higher coverage. phaseolicola 1448A ( Pph 1448A), which has a published, closed genome sequence of 5.93 Mbp. We illustrate the generation of an enhanced-quality draft genome by re-sequencing the plant pathogenic bacterium Pseudomonas syringae pv. Enhanced-quality draft genomes are easily attainable through a combination of small- and large-insert next-generation, paired-end sequencing.
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Here we present a proposal for an “enhanced-quality draft” genome that identifies at least 95% of the coding sequences, thereby effectively providing a full accounting of the genic component of the genome. This lack of uniformity is a particular problem when using standard draft genomes that frequently have large numbers of low-quality sequencing tracts. While groups such as the Genomics Standards Consortium have made strong efforts to promote genome standards there is a still a general lack of uniformity among published draft genomes, leading to challenges for downstream comparative analyses.
Next-generation genomic technology has both greatly accelerated the pace of genome research as well as increased our reliance on draft genome sequences.
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