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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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Journal Article
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
2013
Overview
Unlike hybrid approaches that use multiple libraries for
de novo
assembly, the hierarchical genome-assembly process uses data from only a single long-read SMRT sequencing library to produce high-quality finished microbial genome or BAC assemblies in an automated workflow.
We present a hierarchical genome-assembly process (HGAP) for high-quality
de novo
microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph–based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce
de novo
genome sequence exceeding 99.999% accuracy.
Publisher
Nature Publishing Group US,Nature Publishing Group
