SNP-O-MATIC is software to analyse Solexa reads and compare them to a reference. The core application, findknownsnps, looks at perfect matches of single and paired Solexa reads to a given reference sequence.
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Bioinformatics. 2009 Sep 15;25(18):2434-5. doi: 10.1093/bioinformatics/btp403. Epub 2009 Jul 2.
Manske HM, Kwiatkowski DP.