Abstract Motivation: High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping. Availability: http://snpomatic.sourceforge.net Contact: mm6@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.