SOAPaligner

SOAP2 is a software tool for quickly and accurately aligning short reads to a reference sequence. It utilizes a Burrows-Wheeler Transformation (BWT) compression index to replace the seed strategy of indexing the reference sequence in main memory, resulting in 5.4 GB of memory usage and a 20-30x speed improvement over prior versions. It supports single- and paired-end reads and various text and compressed file formats. A consensus builder is also included for consensus assembly and SNP detection.

Topic

Sequence assembly

Detail

  • Operation: Sequence alignment

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: -

  • Input: -

  • Output: -

  • Contact: soap@genomics.org.cn

  • Collection: -

  • Maturity: -

Publications

  • Using SOAPaligner for Short Reads Alignment
  • Gu S, Fang L, Xu X. Using SOAPaligner for Short Reads Alignment. Curr Protoc Bioinformatics. 2013 Dec 12;44:11.11.1-17. doi: 10.1002/0471250953.bi1111s44. PMID: 26270169.
  • https://doi.org/10.1002/0471250953.bi1111s44
  • PMID: 26270169
  • PMC: -

Download and documentation

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