Short Oligonucleotide Analysis Package: Difference between revisions
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''SOAPindel'' is a tool to find insertions and deletions from next-generation paired-end sequencing data. |
''SOAPindel'' is a tool to find insertions and deletions from next-generation paired-end sequencing data. |
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=== SNP Discovery === |
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''SOAPsnp'' is a consensus sequence builder. This tool uses the output from ''SOAPaligner'' to generate a consensus sequence which enables SNPs to be called on a newly sequenced individual. |
''SOAPsnp'' is a consensus sequence builder. This tool uses the output from ''SOAPaligner'' to generate a consensus sequence which enables [[Single nucleotide polymorphisms|SNPs]] to be called on a newly sequenced individual. |
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=== Structural Variation Discovery === |
=== Structural Variation Discovery === |
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Revision as of 07:46, 9 January 2015
 | The topic of this article may not meet Wikipedia's general notability guideline. (December 2009) |
SOAP (Short Oligonucleotide Analysis Package) is a suite of bioinformatics software tools enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read data.
All programs in the SOAP package may be used free of charge and are distributed under the GPL.
Functionality
The SOAP package can be used to perform the following tasks:
Sequence Alignment
SOAPaligner is specifically designed for fast alignment of short reads and performs favorably with respect to similar alignment tools such as Bowtie and MAQ [1].
Genome Assembly
SOAPdenovo is a short read denovo assembler. It is optimized for short reads such as that generated by Illumina and is capable of assembling large genomes such as the human genome [2]. SOAPdenovo was used to assemble the genome of the giant panda [3].
Indel Discovery
SOAPindel is a tool to find insertions and deletions from next-generation paired-end sequencing data.
SNP Discovery
SOAPsnp is a consensus sequence builder. This tool uses the output from SOAPaligner to generate a consensus sequence which enables SNPs to be called on a newly sequenced individual.
Structural Variation Discovery
SOAPsv is a tool to find structural variations using whole genome assembly.
History
SOAP v1
The first release of SOAP consisted only of the sequence alignment tool SOAPaligner. [4]
SOAP v2
SOAP v2 extended and improved on SOAP v1 by significantly improving the performance of the SOAPaligner tool. Alignment time was reduced by a factor of 20-30, while memory usage was reduced by a factor of 3. Support was added for compressed file formats.
The SOAP suite was expanded to include the new tools: SOAPdenovo, SOAPindel, SOAPsnp, and SOAPsv.
SOAP v3
SOAP v3 extended the alignment tool by being the first short-read alignment tool to utilize GPU processors [5]. As a result of these improvements, SOAPalign significantly outperforms competing aligners Bowtie and BWA in terms of speed.
See also
External links
- http://soap.genomics.org.cn
- http://soap.genomics.org.cn/soap1
- http://bioinformatics.genomics.org.cn
- http://seqanswers.com/forums/showthread.php?t=43
References
- ^ Li, R.; Yu, C.; Li, Y.; Lam, T.-W.; Yiu, S.-M.; Kristiansen, K.; Wang, J. (2009). "SOAP2: an improved ultrafast tool for short read alignment". Bioinformatics. 25 (15): 1966–1967. doi:10.1093/bioinformatics/btp336. ISSN 1367-4803.
- ^ Li, R.; Zhu, H.; Ruan, J.; Qian, W.; Fang, X.; Shi, Z.; Li, Y.; Li, S.; Shan, G.; Kristiansen, K.; Li, S.; Yang, H.; Wang, J.; Wang, J. (2009). "De novo assembly of human genomes with massively parallel short read sequencing". Genome Research. 20 (2): 265–272. doi:10.1101/gr.097261.109. ISSN 1088-9051.
- ^ Li, Ruiqiang; Fan, Wei; Tian, Geng; Zhu, Hongmei; He, Lin; Cai, Jing; Huang, Quanfei; Cai, Qingle; Li, Bo; Bai, Yinqi; Zhang, Zhihe; Zhang, Yaping; Wang, Wen; Li, Jun; Wei, Fuwen; Li, Heng; Jian, Min; Li, Jianwen; Zhang, Zhaolei; Nielsen, Rasmus; Li, Dawei; Gu, Wanjun; Yang, Zhentao; Xuan, Zhaoling; Ryder, Oliver A.; Leung, Frederick Chi-Ching; Zhou, Yan; Cao, Jianjun; Sun, Xiao; Fu, Yonggui; Fang, Xiaodong; Guo, Xiaosen; Wang, Bo; Hou, Rong; Shen, Fujun; Mu, Bo; Ni, Peixiang; Lin, Runmao; Qian, Wubin; Wang, Guodong; Yu, Chang; Nie, Wenhui; Wang, Jinhuan; Wu, Zhigang; Liang, Huiqing; Min, Jiumeng; Wu, Qi; Cheng, Shifeng; Ruan, Jue; Wang, Mingwei; Shi, Zhongbin; Wen, Ming; Liu, Binghang; Ren, Xiaoli; Zheng, Huisong; Dong, Dong; Cook, Kathleen; Shan, Gao; Zhang, Hao; Kosiol, Carolin; Xie, Xueying; Lu, Zuhong; Zheng, Hancheng; Li, Yingrui; Steiner, Cynthia C.; Lam, Tommy Tsan-Yuk; Lin, Siyuan; Zhang, Qinghui; Li, Guoqing; Tian, Jing; Gong, Timing; Liu, Hongde; Zhang, Dejin; Fang, Lin; Ye, Chen; Zhang, Juanbin; Hu, Wenbo; Xu, Anlong; Ren, Yuanyuan; Zhang, Guojie; Bruford, Michael W.; Li, Qibin; Ma, Lijia; Guo, Yiran; An, Na; Hu, Yujie; Zheng, Yang; Shi, Yongyong; Li, Zhiqiang; Liu, Qing; Chen, Yanling; Zhao, Jing; Qu, Ning; Zhao, Shancen; Tian, Feng; Wang, Xiaoling; Wang, Haiyin; Xu, Lizhi; Liu, Xiao; Vinar, Tomas; Wang, Yajun; Lam, Tak-Wah; Yiu, Siu-Ming; Liu, Shiping; Zhang, Hemin; Li, Desheng; Huang, Yan; Wang, Xia; Yang, Guohua; Jiang, Zhi; Wang, Junyi; Qin, Nan; Li, Li; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Wong, Gane Ka-Shu; Olson, Maynard; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun (2009). "The sequence and de novo assembly of the giant panda genome". Nature. 463 (7279): 311–317. doi:10.1038/nature08696. ISSN 0028-0836.
- ^ Li, R.; Li, Y.; Kristiansen, K.; Wang, J. (2008). "SOAP: short oligonucleotide alignment program". Bioinformatics. 24 (5): 713–714. doi:10.1093/bioinformatics/btn025. ISSN 1367-4803.
- ^ Liu, C.-M.; Wong, T.; Wu, E.; Luo, R.; Yiu, S.-M.; Li, Y.; Wang, B.; Yu, C.; Chu, X.; Zhao, K.; Li, R.; Lam, T.-W. (2012). "SOAP3: ultra-fast GPU-based parallel alignment tool for short reads". Bioinformatics. 28 (6): 878–879. doi:10.1093/bioinformatics/bts061. ISSN 1367-4803.