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VAAL | Specific polymorphism discovery in bacteria using massively parallel sequencing

A package to use massively parallel DNA sequence data to identify differences between bacterial genomes at high sensitivity and specificity. VAAL is a variant ascertainment algorithm which found ~98% of differences (including large indels) between pairs of strains from three species while calling no false positives. During evaluation of the performance on the callable polymorphisms, VAAL shows high sensitivity in finding nearly all of the possible callable polymorphisms.

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VAAL classification

VAAL specifications

Unique identifier:
Command line interface
Input data:
Short reads from a ‘sample genome’ and a known sequence for a related ‘reference genome
Computer skills:
Source code URL:
Software type:
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Operating system:

VAAL distribution


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Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Science and Technology / National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research / Medical Research Council Centre for Molecular and Cellular Biology, Department of Biomedical Science, Stellenbosch University, Stellenbosch, South Africa; Department of Molecular Biology and Molecular Genetics, Harvard Medical School, Boston, MA, USA; Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA

Funding source(s)

This work was supported by the National Human Genome Research Institute.

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