New Assembly Method Published for Rapid and Automated Genome Sequencing Using Long-Read, Single Molecule, Real-Time (SMRT(R)) Sequencing
Monday, May 6, 2013
sequence for several microorganisms and a human bacterial artificial chromosome (BAC) clone. As part of the paper, the authors also describe a new consensus algorithm, Quiver, that achieves highly accurate de novo genome sequence results exceeding 99.999% (QV 50) accuracy.
Finished genomes are crucial for understanding microbes and advancing the field of microbiology.ii Previous attempts for obtaining the complete genome sequence of microbes in an automated, high-throughput manner have challenged researchers. For example, with second-generation sequencing methods, short read lengths inhibit the ability to resolve long repeats, resulting in unfinished, fragmented draft assemblies. Further, extreme sequence contexts, such as GC- or AT-rich regions, or palindromic sequences, lead to gaps in draft genome assemblies that cannot be covered using these second-generation methods. As a result,
employed for finishing microbial genomes, but due to its laborious and low-throughput nature this process is slow and expensive.
More recently, hybrid-assembly approaches have been described in which long PacBio reads were used in combination with short-read dataiii,iv. Building on these advances, in this new paper the authors utilize just a single, long-insert shotgun DNA library in conjunction with SMRT Sequencing, thereby removing the need for additional sample preparation and sequencing data sets required for previously described hybrid strategies. A paper describing a similar strategy and assembly results by S. Koren, A. Phillippy, and colleagues from the National Biodefense Analysis and Countermeasures Center,
“This approach can close the large gap that currently exists between ‘draft’ and high-quality ‘finished’ genomes,” said
Pacific Biosciences recently launched the PacBio® RS II — a new SMRT Sequencing system that provides the industry’s highest consensus accuracy and longest reads with double the throughput from the previous version of the system. The PacBio RS II allows scientists to rapidly and cost-effectively generate finished genome assemblies, reveal and understand epigenomes, and characterize genomic variation. The PacBio RS II system, including consumables and software, provides a simple, fast, end-to-end sequencing workflow for applications such as infectious disease and microbiology, agriculture, and understanding rare diseases.
More information is available at www.pacb.com.
About Pacific Biosciences
i Chin et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods doi 10.1038/nmeth.2474.
Maurissa MessierFor Pacific Biosciences 760.539.7417 firstname.lastname@example.org Investors: Trevin RardPacific Biosciences 650.521.8450 email@example.com
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