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SMALT aligns DNA sequencing reads with a reference genome.

   Supported Sequencing Platforms
   Reads from a wide range of sequencing platforms can be processed, for
   example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads
   are supported. There is no support for SOLiD reads.
   The software employs a hash index of short words of up to 20 nucleotides
   sampled at equidistant steps along the reference genome. For each sequencing
   read, potentially matching segments in the reference genome are identified
   from seed matches in the index and subsequently aligned with the read using
   dynamic programming.

Environment Modules

Run module spider smalt to find out what environment modules are available for this application.

System Variables

  • HPC_SMALT_DIR - installation directory
  • HPC_SMALT_BIN - executable directory
  • HPC_SMALT_DOC - user manual directory