VAAL Main Page
VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. On bacterial data sets, it achievies very high sensitivity, and near perfect specificity. VAAL can be used to compare reads from one strain to a reference sequence from another strain. It can also be used to compare reads from two strains to each other, using a third strain to determine homology. For example, we have used VAAL to find a single mutation responsible for bacterial resistance: the output of the program was that single mutation and no others. VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.
- Nightly Build: The current state of development - updated within the last 24 hours.
- Stable Build: The latest stable, trustworthy version of VAAL.
- The VAAL Manual is available
Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.. Nature Methods 2009 Jan;6(1): 67-9.