Development of system to improve the quality of draft assemblies

2017 Fiscal Year Final Research Report

• Project/Area Number: 26430200
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: System genome science
• Research Institution: Institute of Physical and Chemical Research (2015-2017); Kazusa DNA Research Institute (2014)
• Principal Investigator: Kosugi Shunichi 国立研究開発法人理化学研究所, 統合生命医科学研究センター, 研究員 (30365457)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Keywords: アセンブリ / ゲノム

Outline of Final Research Achievements

I constructed genome assemblies with the whole genome sequencing reads from budding yeast, nematoda, and rice, and determined the statistics for the metrics and error properties of the assemblies. Using the likelihood ratio of the alignment properties (i.e., alignment length, alignment identity, and mapping rate of paired-end short reads) between the true and false alignment data, I developed a gap-closing tool, GMcloser, that closes gaps in assemblies with high accuracy. In addition, I developed another too tools, GMvalue and Extrerm. GMvalue determines the metrics of misassemblies including the number of misassembles. Extreme reassembles a preassembled config set by extending the termini of the contigs followed by assembling the extended contigs with overlap-layout-consensus algorithm.

Free Research Field

ゲノム科学