snakemake script to infere orthogroups with fasta-formated genomes as the input. Genomes are annotated with prokka first. Then orthofinder is run.
Requires snakemake and conda3 to be installed.
Please place fasta formated genomes (with .fna extension) in the fna folder.
Run with snakemake --use-conda
If genome files have extension other than .fna please rename them, i.e. with following command:
for i in fna/*.fasta; do mv $i fna/$(basename $i .fasta).fna; done
test_fna folder contains three example sequences of E. coli plasmids, which may be used for testing the pipeline.
- Fasta formated files are modified if neccessary to be consisten with prokka annotation tool.
- If header contains symbols other than alphanumericals and
_they are converted to_ - If header is longer than 20 symbols it is cropped to first 18 symbols and dots are added to the end (i.e.
gi|15829254|ref|NC_002695.1becomesgi|15829254|ref|NC..)
- If header contains symbols other than alphanumericals and
- annotation with Prokka
- fasta files with amino acid sequences are generated from genebank files, gene location and product information is added to headers
- orthogroups inferred with OrthoFinder