Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
Our variant ascertainment algorithm, VAAL, uses massively parallel DNA sequence data to identify differences between bacterial genomes with high sensitivity and specificity. VAAL detected approximately 98% of differences (including large insertion-deletions) 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.
Nusbaum
Chad
C
Broad Institute of Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA.
Ohsumi
Toshiro K
TK
Gomez
James
J
Aquadro
John
J
Victor
Thomas C
TC
Warren
Robert M
RM
Hung
Deborah T
DT
Birren
Bruce W
BW
Lander
Eric S
ES
Jaffe
David B
DB
D000465:Algorithms; D001483:Base Sequence; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics*; D030561:Databases, Nucleic Acid; D011110:Polymorphism, Genetic / Q000235:genetics*; D012680:Sensitivity and Specificity
D004269:DNA, Bacterial