title: Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
abstract: 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.
authors: Pacific Biosciences, Menlo Park, California, USA.
authors: Chen-Shan
authors: CS
authors: Chin
authors: David H
authors: DH
authors: Alexander
authors: Patrick
authors: P
authors: Marks
authors: Aaron A
authors: AA
authors: Klammer
authors: James
authors: J
authors: Drake
authors: Cheryl
authors: C
authors: Heiner
authors: Alicia
authors: A
authors: Clum
authors: Alex
authors: A
authors: Copeland
authors: John
authors: J
authors: Huddleston
authors: Evan E
authors: EE
authors: Eichler
authors: Stephen W
authors: SW
authors: Turner
authors: Jonas
authors: J
authors: Korlach
mesh_terms: D022202:Chromosomes, Artificial, Bacterial; D004926:Escherichia coli / Q000235:genetics; D015723:Gene Library; D016680:Genome, Bacterial; D006801:Humans; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*
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