manual/intro.md
# MiGA: Microbial Genomes Atlas
## What is MiGA?
MiGA is a data management and processing system for microbial genomes and
metagenomes. Its main goal is to provide a uniform system for genome-based
taxonomic classification and diversity studies, but its base can be used for
other purposes.
* [How can MiGA help me?](part1/pitch.md)
* [Who's using MiGA?](part1/use-cases.md)
* [Definitions](glossary.md)
## Getting started with MiGA
MiGA itself doesn't require much but processing large data collections may
require large infrastructures. With that in mind, MiGA is designed to support
both single machines and cluster infrastructures.
* [Requirements](part2/requirements.md)
* [Installation](part2/installation.md)
* [MiGA types](part2/types.md)
* [Input data](part2/input.md)
* [Distances](part2/distances.md)
* [Clustering](part2/clustering.md)
## MiGA Interfaces
You can interact with MiGA through different interfaces. These interfaces have
different purposes, but they also have some degree of overlap, because different
users with different aims sometimes want to do the same thing. The API and the
CLI are the most comprehensive and flexible interfaces, but the other two are
friendlier to humans. MiGA is mostly written in Ruby, with an object-oriented
approach, and all the interfaces are just thin layers atop the Ruby core. That
means that you can write your own interfaces \(or pieces\) if you know how to
talk to these Ruby objects. Sometimes I even use `irb`, which is an interactive
shell for Ruby, but that's mostly for debugging.
* [MiGA API](part3/api.md)
* [MiGA CLI](part3/cli.md)
* [MiGA Web](part3/web.md)
* See also: [Help for MiGA Online](https://help.microbial-genomes.org/)
## Deploying examples
Once you have installed MiGA, you might want to follow one (or several) of these
tutorials to familiarize yourself with the MiGA environment.
* [RefSeq in MiGA](part4/deploy-refseq.md)
* [Build a clade collection](part4/deploy-clade.md)
* [Launching daemons](part4/daemons.md)
* [Setting up MiGA in a cluster](part4/cluster.md)
## MiGA in detail
Ready for more? Here are some technical details for advanced users.
* [Advanced configuration](part5/advanced-configuration.md)
* [MiGA workflow](part5/workflow.md)
* [Metadata](part5/metadata.md)
* [External Software](part5/external.md)
## Workflows
MiGA comes with ready-to-use pre-configured workflows for different analyses:
* [Quality](part6/quality_wf.md)
* [Dereplicate](part6/derep_wf.md)
* [Classify](part6/classify_wf.md)
* [Preprocess](part6/preproc_wf.md)
* [Index](part6/index_wf.md)
* [Summaries](part6/summaries.md)