Nusbaum, ChadOhsumi, Toshiro K.Gomez, JamesAquadro, JohnVictor, Thomas C.Warren, Robert M.Hung, DeborahBirren, Bruce W.Lander, EricJaffe, David B.2009-08-282008Nusbaum, Chad, Toshiro K. Ohsumi, James Gomez, John Aquadro, Thomas C. Victor, Robert M. Warren, Deborah T. Hung, Bruce W. Birren, Eric S. Lander, and David B. Jaffe. 2009. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nature Methods 6, no. 1: 67-69.1548-7091http://nrs.harvard.edu/urn-3:HUL.InstRepos:3228038Our variant ascertainment algorithm, VAAL, uses massively parallel DNA sequence data to identify differences between bacterial genomes with high sensitivity and specificity. VAAL detected B98% of differences (including large insertiondeletions) between pairs of strains from three species while calling no false positives. VAAL also pinpointed a single mutation between Vibrio cholerae genomes, identifying an antibiotic’s site of action by identifying sequence differences between drug-sensitive strains and drug-resistant derivatives.en-US10.1038/nmeth.1286