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