fast, stringent short-read mapping software

 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.
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 SNP-o-matic is a fast, stringent short-read mapping software. It supports a
 multitude of output types and formats, for uses in filtering reads, alignments,
 sequence-based genotyping calls, assisted reassembly of contigs etc.