Workflows

What is a Workflow?

193 Workflows visible to you, out of a total of 193

Purge-duplicate-contigs-VGP6/main

Intergalactic Workflow Commission (IWC)

Purge contigs marked as duplicates by purge_dups.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Created: 31st Oct 2023 at 03:02, Last updated: 29th Jan 2026 at 03:01

metagenomic-raw-reads-amr-analysis/main

Intergalactic Workflow Commission (IWC)

Tests Passing

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).

Type: Galaxy

Creators: ABRomics , Hugo Lefeuvre, abromics-consortium

Submitter: WorkflowHub Bot

Created: 24th Jan 2026 at 03:01

cgmlst-bacterial-genome/main

Intergalactic Workflow Commission (IWC)

Tests Passing

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

Type: Galaxy

Creators: ABRomics , Clea Siguret, Hugo Lefeuvre, abromics-consortium

Submitter: WorkflowHub Bot

Created: 21st Jan 2026 at 03:01

annotation-braker3/main

Intergalactic Workflow Commission (IWC)

This workflow performs genome annotation using Braker3 and evaluates the quality of the annotation with BUSCO and genome annotation statistics.

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

Created: 9th Dec 2025 at 03:01

host-contamination-removal-long-reads/main

Intergalactic Workflow Commission (IWC)

Tests Passing

This workflow takes Nanopore fastq(.gz) files and runs Minimap2 to map the reads against a reference genome (human, by default). It filters the output to keep only the unmapped reads and generates mapping statistics that are aggregated into a MultiQC report.

Type: Galaxy

Creators: Paul Zierep, Bérénice Batut

Submitter: WorkflowHub Bot

Created: 6th Dec 2025 at 03:02

host-contamination-removal-short-reads/main

Intergalactic Workflow Commission (IWC)

Tests Passing

This workflow takes paired-end Illumina fastq(.gz) files and runs Bowtie to map the reads against a reference genome (human, by default) and keep only the reads that do not align. MultiQC is used to aggregate the mapping reports.

Type: Galaxy

Creators: Paul Zierep, Bérénice Batut

Submitter: WorkflowHub Bot

Created: 6th Dec 2025 at 03:01

short-read-qc-trimming/main

Intergalactic Workflow Commission (IWC)

This workflow performs quality control and trimming on paired-end Illumina fastq(.gz) files using fastp and aggregates the quality control reports with MultiQC

Type: Galaxy

Creators: Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

Created: 4th Dec 2025 at 03:02

metagenomic-genes-catalogue/main

Intergalactic Workflow Commission (IWC)

Tests Not available

Metagenomic analysis, from raw reads to gene catalog. Uses Megahit to assemble contigs and Prodgial to predict CDSs on contigs to provide the gene catalog. Finally, functional, taxonomic, and antimicrobial resistance information is provided.

Type: Galaxy

Creators: ABRomics , Hugo Lefeuvre, abromics-consortium

Submitter: WorkflowHub Bot

Created: 30th Nov 2025 at 03:01