MiGA Manual
AboutCodebaseMiGA Online
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main
  • 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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  • Raw reads
  • Trimmed reads
  • Assemblies
  1. Part II: Getting started

Input data

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Last updated 4 years ago

MiGA datasets can be created from three different points: , , and .

The input files can be added through the using miga add or any of the available . Files can also be added through the interface.

Raw reads

Raw (unprocessed) sequencing reads. MiGA can handle different sequencing technologies, but it has been optimized for short reads.

  • Format: FastQ, optionally gzipped (with .gz extension)

  • Workflow step:

Trimmed reads

Sequencing reads already processed to remove low quality or other artifacts. MiGA can handle different sequencing technologies, but has been optimized for short reads.

  • Format: FastA, optionally gzipped (with .gz extension)

  • Workflow step:

Assemblies

Assembled contigs/scaffolds. Ideally, but not necessarily, sequences longer than 1 Kbp.

  • Format: FastA, optionally gzipped (with .gz extension)

  • Workflow step:

CLI
workflows
Web
Raw reads
Trimmed reads
Assemblies
Raw reads
Trimmed FastA
Assembly