milkywhite-mushroom

Scripts to assist with the genome assembly and annotation of Calocybe indica

Scripts

download_fungal_genomes.sh

Python dependencies

• biopython
• pandas

Set up

Clone repo:

git clone https://github.com/Jearce/milkywhite-mushroom.git
cd milkywhite-mushroom

After repo is cloned. Add the repo directory to your PATH.

Then make download_fungal_genomes.sh and extract_and_format_fungi_names.py executeble:

chmod +x download_fungal_genomes.sh
chmod +x extract_and_format_fungi_names.py

Usage

download_fungal_genome.sh takes a single csv file from EnsemblFungi and will use the name of the organisms to download all CDS in fasta format.

Below is the help message:

usage: ./download_fungal_genomes.sh <csv file>
 Any failed downloads are logged to fungal.downloads.log file.

Assembly

Create conda env.

mamba env create -f assembly_env.yaml