Ultrafast SNP-sensitive and Gap-sensitive Alignment of Short Reads to Human Genome via Better Indexing


Grant Data
Project Title
Ultrafast SNP-sensitive and Gap-sensitive Alignment of Short Reads to Human Genome via Better Indexing
Principal Investigator
Professor Lam, Tak Wah   (Principal investigator)
Co-Investigator(s)
Dr Sung Wing Kin   (Co-Investigator)
Dr Li Ruiqiang   (Co-Investigator)
Duration
36
Start Date
2012-08-01
Completion Date
2015-07-31
Amount
626400
Conference Title
Presentation Title
Keywords
algorithm engineering, Bioinformatics algorithms, short read alignment, Text indexing
Discipline
Bioinformatics
Panel
Engineering (E)
Sponsor
RGC General Research Fund (GRF)
HKU Project Code
HKU 713512E
Grant Type
General Research Fund (GRF)
Funding Year
2012/2013
Status
Completed
Objectives
1) New indexing method for SNPs; fast SNP-sensitive alignment tool; 2) Fast and more sensitive gap alignment tool for RNA-Seq data; 3) GPU-based software for fine-grain semi-global alignment.