How do alignment programs perform on sequencing data with varying qualities and from repetitive regions
作者： Xiaoqing Yu , Kishore Guda , Joseph Willis , Martina Veigl , Zhenghe Wang
关键词: Simulated data 、 DNA sequencing 、 Hybrid genome assembly 、 Computer science 、 Sequencing data 、 Data mining 、 Repetitive Regions 、 Quality (business) 、 Genome
摘要: Background Next-generation sequencing technologies generate a significant number of short reads that are utilized to address variety biological questions. However, quite often, tend have low quality at the 3’ end and generated from repetitive regions genome. It is unclear how different alignment programs perform under these cases. In order investigate this question, we use both real data simulated with above issues evaluate performance four commonly used algorithms: SOAP2, Bowtie, BWA, Novoalign.
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Faraz Hach, Fereydoun Hormozdiari, Can Alkan, Farhad Hormozdiari, Inanc Birol, Evan E Eichler, S Cenk Sahinalp, mrsFAST: a cache-oblivious algorithm for short-read mapping Nature Methods. ,vol. 7, pp. 576- 577 ,(2010) , 10.1038/NMETH0810-576
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
Saul B. Needleman, Christian D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins Journal of Molecular Biology. ,vol. 48, pp. 443- 453 ,(1970) , 10.1016/0022-2836(70)90057-4
H. Li, N. Homer, A survey of sequence alignment algorithms for next-generation sequencing. Briefings in Bioinformatics. ,vol. 11, pp. 473- 483 ,(2010) , 10.1093/BIB/BBQ015
Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang, None, SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. ,vol. 25, pp. 1966- 1967 ,(2009) , 10.1093/BIOINFORMATICS/BTP336
H. Jiang, W. H. Wong, SeqMap: mapping massive amount of oligonucleotides to the genome Bioinformatics. ,vol. 24, pp. 2395- 2396 ,(2008) , 10.1093/BIOINFORMATICS/BTN429
H. Li, R. Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics. ,vol. 25, pp. 1754- 1760 ,(2009) , 10.1093/BIOINFORMATICS/BTP324
H. Li, J. Ruan, R. Durbin, Mapping short DNA sequencing reads and calling variants using mapping quality scores Genome Research. ,vol. 18, pp. 1851- 1858 ,(2008) , 10.1101/GR.078212.108
Yangho Chen, Tade Souaiaia, Ting Chen, PerM: Efficient Mapping of Short Sequencing Reads with Periodic Full Sensitive Spaced Seeds Bioinformatics. ,vol. 25, pp. 2514- 2521 ,(2009) , 10.1093/BIOINFORMATICS/BTP486
Korbinian Schneeberger, Gunnar Rätsch, Fabio De Bona, Stephan Ossowski, Optimal spliced alignments of short sequence reads BMC Bioinformatics. ,vol. 9, pp. 1- 2 ,(2008) , 10.1186/1471-2105-9-S10-O7