SOAP2: an improved ultrafast tool for short read alignment

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

SOAP2: an improved ultrafast tool for short read alignment. / Li, Ruiqiang; Yu, Chang; Li, Yingrui; Lam, Tak-Wah; Yiu, Siu-Ming; Kristiansen, Karsten; Wang, Jun.

In: Bioinformatics, Vol. 25, No. 15, 2009, p. 1966-7.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

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, vol. 25, no. 15, pp. 1966-7. https://doi.org/10.1093/bioinformatics/btp336

APA

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), 1966-7. https://doi.org/10.1093/bioinformatics/btp336

Vancouver

Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966-7. https://doi.org/10.1093/bioinformatics/btp336

Author

Li, Ruiqiang ; Yu, Chang ; Li, Yingrui ; Lam, Tak-Wah ; Yiu, Siu-Ming ; Kristiansen, Karsten ; Wang, Jun. / SOAP2: an improved ultrafast tool for short read alignment. In: Bioinformatics. 2009 ; Vol. 25, No. 15. pp. 1966-7.

Bibtex

@article{caee8740914e11de8bc9000ea68e967b,
title = "SOAP2: an improved ultrafast tool for short read alignment",
abstract = "SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn.",
author = "Ruiqiang Li and Chang Yu and Yingrui Li and Tak-Wah Lam and Siu-Ming Yiu and Karsten Kristiansen and Jun Wang",
year = "2009",
doi = "10.1093/bioinformatics/btp336",
language = "English",
volume = "25",
pages = "1966--7",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "15",

}

RIS

TY - JOUR

T1 - SOAP2: an improved ultrafast tool for short read alignment

AU - Li, Ruiqiang

AU - Yu, Chang

AU - Li, Yingrui

AU - Lam, Tak-Wah

AU - Yiu, Siu-Ming

AU - Kristiansen, Karsten

AU - Wang, Jun

PY - 2009

Y1 - 2009

N2 - SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn.

AB - SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn.

U2 - 10.1093/bioinformatics/btp336

DO - 10.1093/bioinformatics/btp336

M3 - Journal article

C2 - 19497933

VL - 25

SP - 1966

EP - 1967

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

SN - 1471-2105

IS - 15

ER -

ID: 13948574