A snakemake script to download ncbi complete genome files, gather them to a directory and discompress them to obtain fasta format files.
The main purpose of this small snakemake script is to download the complete genome files in fasta.gz format for the specified species from the NCBI Refseq database, using the ncbi-genome-download software. Then the fasta.gz files were all put together in a folder and decompressed using pigz to obtain fasta files for the next step of analysis.
The main dependences are ncbi-genome-download, snakemake and pigz. You can create a environment using the ncbi_download.yaml file by:
conda env create -f ncbi_download.yaml
This will create an environment containing all softwares required. To activate this environment, type:
source activate ncbidownload
Just open the .smk file with a editor like notepad++，change line 2 the origanism to which you want to download.
Such as:
organism="Bifidobacterium thermophilum"
Create a .txt file name start_down.txt where you put the script. Then type the following command:
snakemake -s Asdncg.smk -c 4 --jobs 1
If you want to learn more about downloading genomes data, please visit the page of this script's main dependence. ncbi-genome-download. Thanks.