- rsync (linux command, required for downloading NCBI genomes)
- python 3.8 (or greater)
conda install -c conda-forge rsync
# or
sudo apt install rsync
https://pypi.org/project/makura/
install from Pypi
pip install makura
install locally
python setup.py install
install from docker
docker pull hunglin59638/makura
Update the assembly summary and taxonomy information while first using.
makura update
It's ok that you don't run the command, makura will automatically update if the assembly summary is not found.
Download bacteria and fungi genomes with complete assembly level in RefSeq database.
makura download --group bacteria,fungi --assembly-level complete --assembly-source refseq --out_dir /path/to/dir
Print the records of genomes with JSON lines format, default is TAB
makura summary --accession GCF_016700215.2 --as-json-lines
Download genomes with selected taxids
makura download --taxid 2209
If you have many items to input, input a file contains lines is supported. Example: taxid_list.txt
61645
69218
550
makura download --taxid-list taxid_list.txt --out_dir /path/to/dir
Tips:
Running with multiple downloads in parallel is supported (Default: 4).
We set the maximum is 8 to avoid NCBI blocks the downloads.
makura download --group bacteria,fungi --parallel 4
While downloading the genomes, makura can check the MD5 checksum of them.
The MD5 values was stored to a file named md5checksums.txt in output directory.
Using the RESTful API to get assembly summary
- run the API server
docker run --rm -p 5000:5000 hunglin59638/makura:1.1.0 makura api --port 5000
- get the summary of assembly accessions
curl http://localhost:5000/summary?accessions=GCA_002287175.1,GCA_000762265.1
- Creating minimap2 and bwa index using downloaded genomes.
- Downloading genomes by organism name, biosample, bioproject, etc.