The subspecies classification tool assigns the genotype/subtype of a virus, based on the genotype/subtype assignments maintained by the International Committee on Taxonomy of Viruses (ICTV). This tool infers the genotype/subtype for a query sequence from its position within a reference tree (using the pplacer tool with a reference tree and reference alignment, including the query sequence as input, interpretation of the pplacer result is handled by Cladinator.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.
There is one application service specification defined here:
- Subspecies Classification: The Subspecies Classification tool assigns the genotype/subtype of a virus, based on the genotype/subtype assignments maintained by the International Committee on Taxonomy of Viruses (ICTV).
The code in this module provides the BV-BRC application service wrapper scripts for the subspecies classification service as well as some backend utilities:
| Script name | Purpose |
|---|---|
| App-SubspeciesClassification.pl | App script for the subspecies classification service |