Workflows

This workflow performs taxonomic classification of an input sequence collection (e.g., bins from SemiBin2 or MetaBat) using GTDB-Tk and maps the resulting taxonomy to NCBI taxIDs and names to reconcile differences between classification systems.

An example how ISCC codes can be used to verify image analysis steps

Associated Tutorial

This workflows is part of the tutorial Content Tracking and Verification in Galaxy Workflows with ISCC-SUM, available in the GTN

Features

• Includes Galaxy Workflow Tests

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This workflow is executing a BiaPy workflow using a YAML file where the model selection is predefined.

Associated Tutorial

This workflows is part of the tutorial Execute a BiaPy workflow in Galaxy, available in the GTN

Features

• Includes Galaxy Workflow Tests

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Associated Tutorial

This workflows is part of the tutorial GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5).

Purge contigs marked as duplicates by purge_dups.

This workflow starts from metagenomics short-read data and performs, taxonomic profiling (using Sylph), predicts Antibiotic Resistance Genes (ARGs) (using Groot and deepARG), and standardizes ARG annotations (using argNorm).

This workflow performs core genome multilocus sequence typing (cgMLST) on contigs corresponding to one bacterial genome to characterize bacterial strains using curated reference schemes.

Associated Tutorial

This workflows is part of the tutorial M. tuberculosis Variant Analysis, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)

Associated Tutorial

This workflows is part of the tutorial M. tuberculosis Variant Analysis, available in the GTN

Features

• Includes Galaxy Workflow Tests

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