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  • Description

    (Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

    SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

  • Usage

    To list all executables provided by SSAHA2, run: $ sbgrid-list ssaha2 Copy to clipboard
  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install ssaha2 Copy to clipboard Available operating systems: Linux 64, OS X INTEL
  • Primary Citation*

    Z. Ning, A. J. Cox, and J. C. Mullikin. 2001. SSAHA: a fast search method for large DNA databases. Genome Res. 11(10): 1725-1729.

    • *Full citation information available through

  • Keywords


  • Default Versions

    Linux 64:  2.5.5 (2.6 MB)
    OS X INTEL:  2.5.4 (756.5 KB)

  • Other Versions

      Linux 64:

      2.5.3 (776.2 KB)
    • OS X INTEL:

      2.5.1 (2.6 MB)
  • Developers

    Zemin Ning