: The overall goal of this project is to generate high quality assembled genome sequences for high-priority NHGRI sequencing targets. The work will be carried out in Agencourt's large-scale sequencing facility, which operates at exceptionally high efficiency and at a low operating cost due to the advanced automation, informatics and technical developments that have been implemented. The sequencing approach follows the whole genome shotgun (WGS) and assembly paradigm that has been successfully applied to the mouse and other genomes. A high depth of shotgun coverage, including a large number of paired end reads from recombinant plasmids and large insert clones will enable production of a high quality draft assembly (8x Q20 coverage) capable of supporting robust gene prediction and comparative analysis efforts. The sequencing reads will be assembled using the Arachne whole genome assembly software, and additional mapping information will be integrated to refine the supercontig maps. A minimal tiling path of BACs and Fosmids will be constructed to support the selection of clones for finishing. New technologies to improve the overall efficiency will be developed and implemented, along with a novel method for low cost sequence-based genome mapping. All sequence traces will be submitted within 24 hours of generation to the NCBI Trace archive. Assembled contigs will be submitted to public databases within 24 hours of assembly, and technical advances will be shared with other large scale sequencing centers. The genome sequences will be annotated through collaborations with the appropriate user communities and experienced genome analysis experts.
