MiGA types
MiGA types
MiGA has predefined settings and analyses. In order to maximize simplicity and reproducibility while ensuring a wide array of use cases, MiGA uses presets called "types". There are different types of projects and types of datasets:
Project types
When you create a project, the type of project defines which project-wide analyses are going to be executed (and how). The different types are:
Mixed
Symbol: mixed
.
A mixed collection of genomes, metagenomes, and viromes. This is the most basic type of project, with no support for any project-wide analyses. It is intended for projects that are only concerned with datasets preprocessing, e.g., read trimming, assembly, etc.
Genomes
Symbol: genomes
.
A collection of genomes. This is the most typical type of project, storing a set of genomes from different taxonomic groups. It can be useful for anything from indexing a reference database, to create a collection of metagenomic bins, and anything in between.
Clade
Symbol: clade
.
A collection of closely-related genomes (ANI >= 90%). This is a project for a collection of genomes in the same species (or closely-related species) that require higher resolution but don't require support for a large distance range.
Metagenomes
Symbol: metagenomes
.
A collection of metagenomes and/or viromes. This is an experimental type, currently identical to Mixed.
Dataset types
Once you have a project, the type of the datasets define which analyses are going to be executed for that particular entry (and how). The different types are:
Genome
Symbol: genome
.
The genome from an isolate. This is the most typical case, in which you have a genome (complete or draft) from a pure culture (excluding SAGs).
Single-cell genome
Symbol: scgenome
.
A Single-cell Amplified Genome (SAG). This is the particular case in which you are dealing with an amplified genome from a single cell. These datasets typically have very uneven coverage (resulting in very incomplete assemblies) and sometimes have contamination from external DNA.
Population genome
Symbol: popgenome
.
A population genome (including metagenomic bins). This is the type of dataset that includes sequences from different strains of the same species, such as metagenomic bins or metagenomes of highly enriched (but not pure) cultures.
Metagenome
Symbol: metagenome
.
A metagenome (excluding viromes).
Virome
Symbol: virome
.
A viral metagenome.
Query vs reference datasets
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