MiGA Manual
AboutCodebaseMiGA Online
Primary version
Primary version
  • Introduction
  • Part I: What is MiGA?
    • How can MiGA help me?
    • Who is using MiGA?
    • Who is behind MiGA?
    • Definitions
  • Part II: Getting started
    • Requirements
      • Using Homebrew
      • Using apt-get
      • Using Conda
      • Installing from source
      • MyTaxa Utils
    • Installation
    • MiGA types
    • Input data
    • Distances
    • Clustering
  • Part III: Interfaces
    • MiGA API
    • MiGA CLI
    • MiGA Web
  • Part IV: Deploying examples
    • RefSeq in MiGA
    • Build a clade collection
    • Launching daemons
    • Setting up MiGA in a cluster
  • Part V: Additional details
    • Advanced configuration
    • MiGA workflow
    • Metadata
    • External Software
  • Part VI: Workflows
    • Quality
    • Dereplicate
    • Classify
    • Preprocess
    • Index
    • Summaries
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  • 0. Initialize the project
  • 1. Download publicly available genomes
  • 2. Launch the daemon
  1. Part IV: Deploying examples

RefSeq in MiGA

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Last updated 6 years 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 .

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 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 :

miga daemon start -P .
RefSeq in MiGA using BASH example
NCBI API Key
launching daemons