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input.md

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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