SOAP: short oligonucleotide alignment program

We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is...

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Bibliographic Details
Published in:Bioinformatics 2008-03, Vol.24 (5), p.713-714
Main Authors: Li, Ruiqiang, Li, Yingrui, Kristiansen, Karsten, Wang, Jun
Format: Article
Language:English
Subjects:
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Amino Acid
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Summary:We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets. Availability: http://soap.genomics.org.cn Contact: soap@genomics.org.cn
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btn025