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- Title
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
- Authors
Chin, Chen-Shan; Alexander, David H; Marks, Patrick; Klammer, Aaron A; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E; Turner, Stephen W; Korlach, Jonas
- 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.
- Subjects
MICROBIAL genomes; SINGLE molecules; NUCLEOTIDE sequence; ERROR correction (Information theory); DIRECTED acyclic graphs; WAVEGUIDES
- Publication
Nature Methods, 2013, Vol 10, Issue 6, p563
- ISSN
1548-7091
- Publication type
Article
- DOI
10.1038/nmeth.2474