RefSeq in MiGA
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
cd RefSeq
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
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:
miga ncbi_get -P . --reference --api-key ABCD123 -v
Or you can set it globally as an environmental variable before running miga
:
export NCBI_API_KEY=ABCD123
2. Launch the daemon
Now that your data is ready, you can fire up the daemon to start processing the data. For additional details, see launching daemons:
miga daemon start -P .
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