cgatools 1.4.0

The Complete Genomics Analysis Tools (cgatools) is an open source project to provide tools for downstream analysis of Complete Genomics data. The focus is to provide command line utilities. A C++ API is available as well. For information on how to install cgatools, see the install guide. For a discussion of the motivation and design decisions for cgatools, see the methods document.

The general areas of functionality include:

• Genome comparison
  • snpdiff
  • calldiff
  • listvariants (beta)
  • testvariants (beta)
  • junctiondiff (beta)
• Format conversion
  • generatemastervar (beta)
  • map2sam
  • evidence2sam (beta)
• Annotation
  • join (beta)
  • junctions2events (beta)
• Reference tools
  • fasta2crr
  • crr2fasta
  • listcrr
  • decodecrr