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VAAL (variant ascertainment algorithm)

eagle-i ID

http://harvard.eagle-i.net/i/0000013a-6ae5-c1d3-5088-2eef80000000

Resource Type

  1. Algorithmic software component

Properties

  1. Resource Description
    "VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. On bacterial data sets, it achieves 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."
  2. Additional Name
    variant ascertainment algorithm
  3. Contact
    CRDHELP
  4. Manufacturer
    Broad Institute
  5. Used by
    Broad Institute
  6. Operating System
    UNIX/LINUX
  7. Data Input
    Genomic Sequences (multiple genomes)
  8. Data Output
    Comparison of Genomes
  9. Software purpose
    Sequence comparison objective
  10. Related Publication or Documentation
    VAAL Manual
  11. Related Publication or Documentation
    Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
  12. Website(s)
    ftp://ftp.broadinstitute.org/pub/crd/VAAL/
  13. Related Technique
    Data analysis
  14. Coded in
    Java
 
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