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The following pipeline evolved from the script developed by Miguel Pinheiro, following collaboration with Souad Alateah and operating on her mycobateria samples: M. Absessus and M. Tuberculosis.

The aim of the evolution were as follows:

  • High resolution, pairwise SNP calling between the samples.
  • Parallel launching of the program using Gridengine's DRMAA python library.
  • Taking advantage of recent (2017, version 1.5) improvements in the samtools/bcftools toolkit.

These aims do not however mean that earlier analyses are invalid, but rather they were less precise with lower resolution. For example one of the key problems is the high similarilty between the samples. Often they are almost identical, and the aim here was to refine and improve the method so that these samples could be more distinguishable in terms of their SNP mutations.