A Nextflow pipeline that detects and reports the "Differences between Pairs of Isolates"
Development for the "Ost er ikke Ost Project"
- Takes a csv file defining pair of assemblies to compare.
- Annotates each individual assembly with bakta.
- Choses the longest assembly for each pair and defines that the longuest assembly will be used as reference (python script)
- Runs nucdiff, (based on MUMmer3) to determine the differences between each pair of isolates
- Wrangles and transform file format of annotated vcf (python script)
- Annotates the variants detected for each pair with vcf-annotator
- Wrangles and add all the results (from nucdiff, vcf-annotator, and Bakta annotations) in a sqlite database (2 python scripts).
Workflow:
Under development. Can still require adjustments, and might be developped further. Post pipeline analysis workflow under development.