Skip to content

Azimuth Module Pipeline Specification

Pipeline Details

  • Name: Azimuth Module
  • Pipeline UUID: 9cb230164ffc4f638bbad3df041689db
  • Version: 1.0.2
  • View Pipeline:

Overview

Azimuth Module pipeline is designed for query-reference mapping algorithm for annotating single-cell data. It automates the annotation process by mapping query single-cell datasets to established reference atlases, enabling rapid and accurate cell type identification.

Key Use cases:

  • Single-cell RNA-seq Annotation: Automated cell type annotation for new single-cell datasets using established reference atlases.
  • Cross-dataset Integration: Mapping cells from new experiments to well-characterized reference populations.
  • Cell Type Discovery: Identifying and classifying cell populations in complex single-cell datasets.

Features

  • Reference-based Annotation: Leverages pre-built reference atlases with established cell type annotations for accurate classification.
  • Seurat Integration: Built on the Seurat framework for seamless integration with existing single-cell analysis workflows.
  • High-speed Mapping: Uses Annoy indexing for fast approximate nearest neighbor searches during cell mapping.
  • Containerized Environment: Runs in a standardized Docker container (quay.io/viascientific/azimuth:1.0.0) ensuring reproducibility.
  • Public Reference Library: Access to publicly available reference datasets through the HubMAP Consortium.

Input/Output Specification

Inputs

Required

Query Seurat Object

  • Description: Input single-cell dataset as a Seurat object containing the cells to be annotated.
  • Format: .rds (R data serialization format)
  • Example File Path: /path/to/input/query_data.rds

Reference Seurat Object

  • Description: Pre-processed reference atlas containing annotated cell populations for mapping.
  • Format: .rds (R data serialization format)
  • Example File Path: /path/to/reference/ref.rds

Reference Index File

  • Description: Annoy index file for the reference dataset enabling fast approximate nearest neighbor searches.
  • Format: .annoy
  • Example File Path: /path/to/reference/idx.annoy

Outputs

Reported Outputs

  • Annotated Seurat Object:
  • Description: Query Seurat object with added cell type annotations based on reference mapping
  • Format: .rds
  • Example File Path: /output/directory/sample_annotated.rds
  • Visualization App: Seurat, Single Cell Portal, Cell Browser
  • Location: Output Folder

Associated Processes

References & Additional Documentation