MiGA Manual
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Introduction
Part I: What is MiGA?
Part II: Getting started
Requirements
Installation
MiGA types
Input data
Distances
Clustering
Part III: Interfaces
Part IV: Deploying examples
Part V: Additional details
Part VI: Workflows
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Input data
MiGA datasets can be created from three different points:
Raw reads
,
Trimmed reads
, and
Assemblies
.
The input files can be added through the
CLI
using
miga add
or any of the available
workflows
. Files can also be added through the
Web
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
:
Raw reads
​
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
:
Trimmed FastA
​
Assemblies
Assembled contigs/scaffolds. Ideally, but not necessarily, sequences longer than 1 Kbp.
Format
: FastA, optionally gzipped (with .gz extension)
Workflow step
:
Assembly
​
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Distances
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Contents
Raw reads
Trimmed reads
Assemblies