Workflows
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qcif/taxodactyl is a modular, reproducible Nextflow workflow for the conservative taxonomy assignment to DNA sequences, designed for high-confidence, auditable results in biosecurity and biodiversity contexts. The workflow integrates multiple bioinformatics tools and databases, automates best-practice analysis steps, and produces detailed reports with supporting evidence for each taxonomic assignment.
Workflow Overview
The pipeline orchestrates a series of analytical steps, each encapsulated ...
Type: Nextflow
Creators: Magdalena Antczak, Cameron Hyde, Lanxi (Daisy) Li, Valentine Murigneux, Sarah Williams, Michael Thang, Bradley Pease, Shaun Bochow, Grace Sun
Submitter: Magdalena Antczak
Type: Nextflow
Creators: Alem Gusinac, Thomas Ederveen, Jos Boekhorst, Annemarie Boleij
Submitter: Alem Gusinac
Prediction of HLA binding for verified candidates
Associated Tutorial
This workflows is part of the tutorial Neoantigen 5a: Predicting HLA Binding, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
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Merging Fusion and non-normal databases + Discovery peptidomics using FragPipe
Associated Tutorial
This workflows is part of the tutorial Neoantigen 2: Database merge and FragPipe discovery, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Create a protein Fusion database through the Arriba workflow
Associated Tutorial
This workflows is part of the tutorial Neoantigen 1a: Fusion-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search
Associated Tutorial
This workflows is part of the tutorial Neoantigen 3: PepQuery2 Verification, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Annotating the novel peptides
Associated Tutorial
This workflows is part of the tutorial Neoantigen 4: Variant Annotation, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): GalaxyP ...
Predict binding using IEDB and check novelty peptides with PepQuery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Generating non-reference protein database for FragPipe discovery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 1b: Non-Reference-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Pathogens of all samples report generation and visualization
Associated Tutorial
This workflows is part of the tutorial Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition, available in the GTN
Features
- Includes a [Galaxy Workflow ...