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Rauf Salamzade edited this page Jul 16, 2021 · 3 revisions

Welcome to the ConSequences wiki!

ConSequences is a Python written suite designed to identify highly conserved and contiguous long stretches of DNA shared between two independent DNA molecules.

It consists of three programs:

  1. delineateSegmentsOnReference.py : This program will take a reference scaffold and identify conserved and contiguous segments it shares with one or more query scaffolds.
  2. generateReferenceMSA.py : This program will generate a reference-based MSA for a segment of interest using results from delineateSegmentsOnReference.py.
  3. querySegmentInRawReads.py : This program will use a segment MSA(s) (as generated by generateReferenceMSA.py) and check if some sample's raw sequencing data shows signs of having the assembly path for the segment.

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