selection-an-application.md

description
What application can help me in MiGA @ XSEDE?

Selecting an Application

Different applications in MiGA @ XSEDE automate commonly used workflows in MiGA. Explore the different tabs to identify the workflow that works for you.

{% hint style="info" %} Important: Whenever possible, it's always better to submit a single task with many genomes instead of one task per genome {% endhint %}

{% tabs %} {% tab title="Indexing" %}

Database Indexing

Index a collection of genomes to use as a custom MiGA database to query an unknown genome against this database or search the genomes of the database against each other by calculating the all-vs-all AAI and ANI matrixes.

{% page-ref page="applications/database-indexing.md" %} {% endtab %}

{% tab title="Classification" %}

Genome Classification

Classify query genomes against the TypeMat MiGA genome database as a reference: All genomes from prokaryotic type material available in NCBI.

{% page-ref page="applications/genome-classification.md" %} {% endtab %}

{% tab title="Typing " %}

Genome Typing

Perform a fine sequence (Average Nucleotide Identity or ANI) and gene content diversity analysis for genome-based typing of query genomes within a well-characterized species.

{% page-ref page="applications/genome-typing.md" %} {% endtab %}

{% tab title="Dereplication" %}

Genome Dereplication

Dereplicate a set of genomes using a threshold for ANI (Average Nucleotide Identity) or AAI (Average Amino Acid Identity).

{% page-ref page="applications/genome-dereplication.md" %} {% endtab %} {% endtabs %}