Supported Applications


  • 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.

  • 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

  • Categories


  • Default Versions

    Linux 64 2.5.5
    OS X INTEL 2.5.4

  • Other Available Versions

    Linux 32 2.5.3
    Linux 64 2.5.3
    OS X INTEL 2.5.1

  • Developers

    Zemin Ning.