Pacific Biosciences of California, Inc.
Hierarchical genome assembly method using single long insert library

Abstract:

The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT.RTM.) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT.RTM. cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT.RTM. Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT.RTM. sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy. The methods are typically performed on a computer and comprise an algorithm that constructs sequence alignment graphs from pairwise alignment of sequence reads to a common reference.