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taylorreiter/download_ncbi_fungi.md

Created October 20, 2017 20:22
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Download NCBI fungal genomes from refseq and genbank
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download_ncbi_fungi.md

Create a virtual environment and install ncbi-genome-download

cd ~
python2.7 -m virtualenv ncbi-genome-downloadEnv
source ncbi-genome-downloadEnv/bin/activate
cd ncbi-genome-downloadEnv
git clone https://github.com/kblin/ncbi-genome-download.git
cd ncbi-genome-download
pip install .
source ncbi-genome-downloadEnv/bin/activate

Download the genomes from genbank and refseq

cd ~/fungal_genomes
mkdir ncbi-genome-downloads-fungi
cd ncbi-genome-downloads-fungi
ncbi-genome-download -s genbank -l all -F fasta fungi
ncbi-genome-download -s refseq -l all -F fasta fungi
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