SOAP2: an improved ultrafast tool for short read alignment

• Published in: Bioinformatics Vol. 25; no. 15; pp. 1966 - 1967
• Main Authors: Li, Ruiqiang, Yu, Chang, Li, Yingrui, Lam, Tak-Wah, Yiu, Siu-Ming, Kristiansen, Karsten, Wang, Jun
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.08.2009; Oxford Publishing Limited (England)
• Subjects: Biological and medical sciences; Computational Biology - methods; Fundamental and applied biological sciences. Psychology; General aspects; Genome, Human; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software

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 r...