SOAP: short oligonucleotide alignment program

• Published in: Bioinformatics Vol. 24; no. 5; pp. 713 - 714
• Main Authors: Li, Ruiqiang, Li, Yingrui, Kristiansen, Karsten, Wang, Jun
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.03.2008; Oxford Publishing Limited (England)
• 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; Bioinformatics; Oligonucleotide
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btn025

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