bigdatabiology/ena-mirror

Mirror selected ENA data locally

Mirror selected ENA data locally

This was developed to support the following publication:

Coelho, L.P., Alves, R., del Río, Á.R. et al. Towards the biogeography of prokaryotic genes. Nature 601, 252–256 (2022). https://doi.org/10.1038/s41586-021-04233-4

Please cite this publication if you use this tool.

To use, create a TSV file called studies.txt with the following columns (first row should be column headers):

study_accession	directory_name	reference	comment

Then, run jug execute to retrieve all the data. If you later add more rows, Jug will ensure that only missing data will be downloaded.

The file config.py adds a fews configuration options. You can start with the configuration in config-example.py and edit it to suit your needs. In particular, using aspera, which is turned off by default, can significantly speed up downloads.

Dependencies

• pandas
• requests
• jug