SMALT aligns DNA sequencing reads with a reference genome.
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.
A mode for the detection of split (chimeric) reads is provided. Multi-threaded program execution is supported.