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mrFAST: micro-read Fast Alignment Search Tool.

mrFAST is designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.

Output in SAM format
Indels up to 8 bp (4 bp deletions and 4 bp insertions)
Paired-end mapping
- Discordant option to generate mapping file ready for VariationHunter to detect structural variants.
One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq
Matepair library mapping (long inserts with RF orientation).