國立清華大學

資訊工程學系

Department Of Computer Science

National Tsing Hua University

專題演講

SEMINAR

主 講 人： Prof. Siu-Ming Yiu (University of Hong Kong)

Dr. Thomas K. F. Wong (University of Hong Kong)

 題  目：1. Binning metagenomic data: issues and solutions

        2. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

 時  間：101年6月12日(二) AM 10:00-12:00

DATE

 地    點：資電館R431

PLACE

連絡人：韓永楷 教授

敬請踴躍參加

Abstract

1.

     Micro-organisms in a habitat may interact with one another and affectthe metabolism of their host. Previous findings show that some of these microbes are related to diseases. Analysis of the collective genomes of all micro-organisms from an environmental sample (also known as metagenomics) is an emerging research area. The advances in sequencing technologies enable researchers to produce reads form this collection of genomes in a cost-effective manner. To analyze these reads, a fundamental problem is to cluster these reads into different groups so that reads from the same type of species are put together. In this talk, we will discuss the difficulties of this problem and give an overview on the metacluster suite, developed by our research group, that attempts to solve the problem.

2.

     SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic
 improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.