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Short Oligonucleotide Analysis Package SOAP

Alternative name: SOAP2 | SOAP2

Aligns short reads with a reference sequence. SOAP can find all alignments with k mismatches, where k is chosen from 0 to 3. When aligning length-100 reads with the human genome, SOAP is the first software that can find all 3-mismatch alignments in tens of seconds per one million reads. SOAPaligner is a part of SOAP that allows an ultrafast and memory-efficient alignment of massive short sequencing reads.

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SOAP classification

SOAP specifications

Software type:
Restrictions to use:
Output format:
Tab-delimited text, SAM
Programming languages:
Computer skills:
Command line interface
Input format:
Operating system:


  • SOAPaligner

SOAP distribution


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SOAP support


  • SOAP3 <>
  • Tak-Wah Lam <>
  • Yingrui Li <>
  • Ruiqiang Li <>


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HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, China; School of Computer Science, National University of Defense Technology, Changsha, Hunan, China; BGI-Shenzhen, Shenzhen, Guangdong, China; Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China; Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA

Funding source(s)

Supported by RGC General Research Fund 10612042, Hong Kong ITF Grant GHP/011/12 and the GRF Grant HKU-713512E.

Link to literature

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