Pharokka for phage annotation

[hoelzer]

Paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac776/6858464?login=false

Code: https://github.com/gbouras13/pharokka

I build a container already: docker run --rm nanozoo/pharokka:1.1.0--46a5c6b pharokka.py --help

And I also installed the necessary databases in the container (they are small). So it should be possible to run the tool w/o downloading the databases and just specifying:

pharokka.py -i assembly.fasta -o output -t 4 -d pharokka_database_v1.0.0/

Attention: there seems to be a parameter for multiFASTA (metagenomic) input activated via -m

[mult1fractal]

Nice 👍🏼 Thank you Martin!

[mult1fractal]

• use pharokka as default annotation
• get results from checkv
• create map from contigs with completeness above 75%

[mult1fractal]

integrated with #195