Segminator II
Segminator II has been developed and implemented by John Archer, as part of a project funded by the BBSRC (project grant: BB/H012419/1) that is supervised by David Robertson and Andrew Rambaut. It is a software for the characterization of viral read data that is generated on next generation sequencing platforms including: 454 Life Sciences, Illumina, Ion Torrent and Pacific Biosciences.

Figure 1: Main display area of Segminator II

Notable features of the software include:
  • the seamless mapping and aligning of read data to a reference sequence,
  • the association of multiple datasets to a single reference sequence,
  • the per site coverage, entropy and base frequencies, along with the ability to query sites based on the latter,
  • codon frequencies and consensus sequence generation,
  • phylogenetic inference,
  • read visualization and,
  • a bayesian framework for platform error correction.(new)
Additionally the software boasts a rich and interactive graphical user interface, specialized data storage structures to increase the efficency of memory usage as well as continuous support and development.