Evaluation and comparison of multiple aligners for next-generation sequencing data analysis.
Next-generation sequencing (NGS) technology has rapidly advanced and generated the massive data volumes. To align and map the NGS data, biologists often randomly select a number of aligners without concerning their suitable feature, high performance, and high accuracy as well as sequence variations and polymorphisms existing on reference genome. This study aims to systematically evaluate and compare the capability of multiple aligners for NGS data analysis. To explore this capability, we firstly performed alignment algorithms comparison and classification. We further used long-read and short-read datasets from both real-life and in silico NGS data for comparative analysis and evaluation of these aligners focusing on three criteria, namely, application-specific alignment feature, computational performance, and alignment accuracy. Our study demonstrated the overall evaluation and comparison of multiple aligners for NGS data analysis. This serves as an important guiding resource for biologists to gain further insight into suitable selection of aligners for specific and broad applications.
Center for Systems Biology, Soochow University, 1st Shizi Street, Suzhou, Jiangsu 215006, China ; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
Jing
J
Shang
Center for Systems Biology, Soochow University, 1st Shizi Street, Suzhou, Jiangsu 215006, China ; School of Computer Science and Technology, Soochow University, Suzhou 215006, China.
Fei
0000-0002-2226-2859
F
Zhu
Center for Systems Biology, Soochow University, 1st Shizi Street, Suzhou, Jiangsu 215006, China.
Wanwipa
0000-0003-3805-0719
W
Vongsangnak
Center for Systems Biology, Soochow University, 1st Shizi Street, Suzhou, Jiangsu 215006, China.
Yifei
0000-0003-1979-9070
Y
Tang
Center for Systems Biology, Soochow University, 1st Shizi Street, Suzhou, Jiangsu 215006, China.
Wenyu
W
Zhang
Center for Systems Biology, Soochow University, 1st Shizi Street, Suzhou, Jiangsu 215006, China.
Bairong
B
Shen
D000465:Algorithms; D030561:Databases, Nucleic Acid; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*