RefSeq in MiGA

Last updated 4 months ago

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 .