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NorwegianVeterinaryInstitute / DPI

Differences between Pairs of Isolates
BSD 3-Clause "New" or "Revised" License
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DPI

A Nextflow pipeline that detects and reports the "Differences between Pairs of Isolates"

Development for the "Ost er ikke Ost Project"

  1. Takes a csv file defining pair of assemblies to compare.
  2. Annotates each individual assembly with bakta.
  3. Choses the longest assembly for each pair and defines that the longuest assembly will be used as reference (python script)
  4. Runs nucdiff, (based on MUMmer3) to determine the differences between each pair of isolates
  5. Wrangles and transform file format of annotated vcf (python script)
  6. Annotates the variants detected for each pair with vcf-annotator
  7. Wrangles and add all the results (from nucdiff, vcf-annotator, and Bakta annotations) in a sqlite database (2 python scripts).

Workflow: Overivew of Nexflow Pipeline

Warning:

Under development. Can still require adjustments, and might be developped further. Post pipeline analysis workflow under development.