Short Oligonucleotide Analysis Package

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 [1] 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

References

  1. ↑ 1.0 1.1 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. PMID 19497933.
  2. ↑ 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. PMC 2813482. PMID 20019144.
  3. ↑ 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. PMC 3951497. PMID 20010809.
  4. ↑ 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. PMID 18227114.
  5. ↑ 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.