The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner
Open accessAbstract
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.
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Cites
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Cited by
Li, D., Luo, R., Liu, C.-M., Leung, C.-M., Ting, H.-F., Sadakane, K., Yamashita, H., & Lam, T.-W. (2016) · Methods · doi:10.1016/j.ymeth.2016.02.020 · Cited by 2,079
Self-citationTraining health professionals in shared decision-making: An international environmental scan
Légaré, F., Politi, M. C., Drolet, R., Desroches, S., Stacey, D., & Bekker, H. (2012) · Patient Education and Counseling · doi:10.1016/j.pec.2012.01.002 · Cited by 289
Bejan, C. A., Angiolillo, J., Conway, D., Nash, R., Shirey-Rice, J. K., Lipworth, L., Cronin, R. M., Pulley, J., Kripalani, S., Barkin, S., et al. (2018) · Journal of the American Medical Informatics Association · doi:10.1093/jamia/ocx059 · Cited by 106
De Silva, D., Ranasinghe, W., Bandaragoda, T., Adikari, A., Mills, N., Iddamalgoda, L., Alahakoon, D., Lawrentschuk, N., Persad, R., Osipov, E., et al. (2018) · PLOS ONE · doi:10.1371/journal.pone.0205855 · Cited by 86
Mária, J., & Ingrid, Ž. (2017) · Food & Function · doi:10.1039/c7fo00161d · Cited by 71
Metadata
- Authors
- Luo, R., Wong, T., Zhu, J., Liu, C.-M., Zhu, X., Wu, E., Lee, L.-K., Lin, H., Zhu, W., Cheung, D. W., Ting, H.-F., Yiu, S.-M., Peng, S., Yu, C., Li, Y., Li, R., & Lam, T.-W.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-05-31
- Volume
- 8
- Issue
- 5
- Pages
- e65632
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2015831381
- Cited by
- 425
- References
- 27
- FWCI
- 21.65
- Type
- journal article
- Language
- en
- Open access
- gold
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- Luo, R., Wong, T., Zhu, J., Liu, C.-M., Zhu, X., Wu, E., Lee, L.-K., Lin, H., Zhu, W., Cheung, D. W., Ting, H.-F., Yiu, S.-M., Peng, S., Yu, C., Li, Y., Li, R., & Lam, T.-W. (2013). SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE. https://doi.org/10.1371/journal.pone.0065632
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