phiweger / ideel Goto Github PK

This repo builds on code by Mick Watson who wrote a blog post and follow up about a quick way to test the viability of a (long-read) assembly.

• Snakemake
• Prodigal
• Diamond
• R (including libraries readr and ggplot2)

You will need a Diamond index like UniProt TREMBL.

Clone the repo.

The output of the workflow will be written to --directory. In there, make a directory called "genomes", put assemblies in there with .fa file extension

Edit the config.json file, specifying e.g. the path to the Diamond database.

Then:

# http://snakemake.readthedocs.io/en/stable/executable.html
# http://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html
snakemake --configfile config.json --directory ~/tmp/ --cores 4
# per default, Snakemake uses only 1 CPU core