> For the complete documentation index, see [llms.txt](https://manual.microbial-genomes.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://manual.microbial-genomes.org/master/part4/deploy-refseq.md).

# 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](https://github.com/bio-miga/miga/tree/46281f59136d6237b8629ae9f5017a63d9bfbe72/manual/part4/deploy-refseq-bash.md).

## 0. Initialize the project

```bash
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.

```bash
miga ncbi_get -P . --reference -v
```

It is strongly recommended to use an [NCBI API Key](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/) to increase the number of allowed requests. Once you obtain one, you can pass it as an argument:

```bash
miga ncbi_get -P . --reference --api-key ABCD123 -v
```

Or you can set it globally as an environmental variable before running `miga`:

```bash
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](/master/part4/daemons.md):

```bash
miga daemon start -P .
```


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