MiGA Manual
AboutCodebaseMiGA Online
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  • 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 4 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 -T Archaea

Of course, you can repeat for -T Bacteria to get all prokaryotic genomes.

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 -T Archaea

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