SMALT

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Description

smalt website  

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.

Strategy

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.

Documentation

http://www.sanger.ac.uk/resources/software/smalt/

Required Modules

Serial

  • smalt

System Variables

  • HPC_SMALT_DIR





Validation

  • Validated 4/5/2018