In this tutorial, we will create a genomes project including all the representative genomes available in RefSeq using MiGA alone. If you want to explore a more manual approach using bash, see the RefSeq in MiGA using BASH example.
0. Initialize the project
miga new -P RefSeq -t genomes
1. Download publicly available genomes
Re-running and updating: If the following code fails at any point, for example due to a network interruption, you can simply re-run it, and it will take it from where it failed.
miga ncbi_get -P . --reference -v -T Archaea
Of course, you can repeat for -T Bacteria to get all prokaryotic genomes.
It is strongly recommended to use an NCBI API Key to increase the number of allowed requests. Once you obtain one, you can pass it as an argument: