Silicon Graphics, Incorporated

Pacific Biosciences for California, Inc.

David Alexander

Stephen Wilson Turner

Martin M Deneroff

Patrick Marks

Chen-Shan Chin

Kumar Venkatasubramaniam

Michael E Anderson

Aaron Klammer

Richard G Bahr

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&#xae;) 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&#xae; cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT&#xae; Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT&#xae; 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.

Hierarchical genome assembly method using single long insert library

A dynamic random access memory (DRAM) single in-line memory module (SIMM) having optimized physical dimensions achieves high speed and high storage capacity. The DRAM SIMM has a printed circuit board with a multi-contact connector, a plurality of DRAM sets, each set having a plurality of DRAM chips mounted on the printed circuit board, and a plurality of buffers which are also mounted on the printed circuit board. The number of buffers is equal to the number of DRAM sets. Various standard DRAM chips can be used on the SIMM to achieve different performance and storage capacity, while maintaining plug compatibility of the multi-contact connector with a memory board. The buffers buffer the control and address signals for the DRAM chips, which is necessary to keep control and address signal integrity due to the number of DRAMS. The buffers permit each DRAM to receive the necessary control and address signals in a more synchronized fashion, so that relative delays are well controlled. The multi-contact connector has a first group of pins for receiving control and address signals, a second group of pins for data input/output signals, a third group of pins for indicating the type code of the SIMM, and a fourth group of pins for power and ground connections.

High memory capacity DRAM SIMM

Growing community of inventors

Mountain View, CA, United States of America

David Alexander