Quality-score guided error correction for short-read sequencing data using CUDA

被引：7

作者：

Shi, Haixiang ^{[1
]}

Schmidt, Bertil ^{[1
]}

Liu, Weiguo ^{[1
]}

Mueller-Wittig, Wolfgang ^{[1
]}

机构：

[1] Nanyang Technol Univ, Sch Comp Engn, Singapore 639798, Singapore

来源：

ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS | 2010年 / 1卷 / 01期

关键词：

DNA sequencing; CUDA; high-through short-read assembly; bioinformatics; TECHNOLOGY;

D O I：

10.1016/j.procs.2010.04.125

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

Recently introduced new sequencing technologies can produce massive amounts of short-read data. Detection and correction of sequencing errors in this data is an important but time-consuming pre-processing step for de-novo genome assembly. In this paper, we demonstrate how the quality-score value associated with each base-call can be integrated in a CUDA-based parallel error correction algorithm. We show that quality-score guided error correction can improve the assembly accuracy of several datasets from the NCBI SRA (Short-Read Archive) in terms of N50-values as well as runtime. We further propose a number of improvements of to our previously published CUDA-EC algorithm to improve its runtime by a factor of up to 1.88. (C) 2010 Published by Elsevier Ltd.

引用

页码：1123 / 1132

页数：10

共 17 条

[1] ALLPATHS: De novo assembly of whole-genome shotgun microreads [J].

Butler, Jonathan ;

MacCallum, Iain ;

Kleber, Michael ;

Shlyakhter, Ilya A. ;

Belmonte, Matthew K. ;

Lander, Eric S. ;

Nusbaum, Chad ;

Jaffe, David B. .

GENOME RESEARCH, 2008, 18 (05) :810-820

[2] Fragment assembly with short reads [J].

Chaisson, M ;

Pevzner, P ;

Tang, HX .

BIOINFORMATICS, 2004, 20 (13) :2067-2074

[3] Short read fragment assembly of bacterial genomes [J].

Chaisson, Mark J. ;

Pevzner, Pavel A. .

GENOME RESEARCH, 2008, 18 (02) :324-330

[4] De novo fragment assembly with short mate-paired reads: Does the read length matter? [J].

Chaisson, Mark J. ;

Brinza, Dumitru ;

Pevzner, Pavel A. .

GENOME RESEARCH, 2009, 19 (02) :336-346

[5] Substantial biases in ultra-short read data sets from high-throughput DNA sequencing [J].

Dohm, Juliane C. ;

Lottaz, Claudio ;

Borodina, Tatiana ;

Himmelbauer, Heinz .

NUCLEIC ACIDS RESEARCH, 2008, 36 (16)

[6] Summary cache: A scalable wide-area Web cache sharing protocol [J].

Fan, L ;

Cao, P ;

Almeida, J ;

Broder, AZ .

IEEE-ACM TRANSACTIONS ON NETWORKING, 2000, 8 (03) :281-293

[7] De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer [J].

Hernandez, David ;

Francois, Patrice ;

Farinelli, Laurent ;

Osteras, Magne ;

Schrenzel, Jacques .

GENOME RESEARCH, 2008, 18 (05) :802-809

[8] The impact of next-generation sequencing technology on genetics [J].

Mardis, Elaine R. .

TRENDS IN GENETICS, 2008, 24 (03) :133-141

[9] Bioinformatics challenges of new sequencing technology [J].

Pop, Mihai ;

Salzberg, Steven L. .

TRENDS IN GENETICS, 2008, 24 (03) :142-149

[10] A fast hybrid short read fragment assembly algorithm [J].

Schmidt, Bertil ;

Sinha, Ranjan ;

Beresford-Smith, Bryan ;

Puglisi, Simon J. .

BIOINFORMATICS, 2009, 25 (17) :2279-2280

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