> For the complete documentation index, see [llms.txt](https://manual.microbial-genomes.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://manual.microbial-genomes.org/master/part2/input.md).

# Input data

MiGA datasets can be created from three different points: [Raw reads](/master/part2/input.md#raw-reads), [Trimmed reads](/master/part2/input.md#trimmed-reads), and [Assemblies](/master/part2/input.md#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](/master/part6.md). 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](/master/part5/workflow.md#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](/master/part5/workflow.md#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](/master/part5/workflow.md#assembly)