# Input data

MiGA datasets can be created from three different points: [Raw reads](#raw-reads), [Trimmed reads](#trimmed-reads), and [Assemblies](#assemblies).

The input files can be added through the [CLI](https://github.com/bio-miga/miga/tree/0413f0c757dafd1c3f434abbb30b61514c2868d8/manual/part3/cli.md) using `miga add` or any of the available [workflows](https://manual.microbial-genomes.org/master/part6). Files can also be added through the [Web](https://github.com/bio-miga/miga/tree/0413f0c757dafd1c3f434abbb30b61514c2868d8/manual/part3/web.md) 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](https://manual.microbial-genomes.org/master/part5/workflow#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](https://manual.microbial-genomes.org/master/part5/workflow#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](https://manual.microbial-genomes.org/master/part5/workflow#assembly)