Workflows

What is a Workflow?
195 Workflows visible to you, out of a total of 195
cgmlst-bacterial-genome/main

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

annotation-braker3/main

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

host-contamination-removal-long-reads/main

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

host-contamination-removal-short-reads/main

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

short-read-qc-trimming/main

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

metagenomic-genes-catalogue/main

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

nf-core/bacass

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite with ...

Type: Nextflow

Creator: Andreas Wilm

Submitter: WorkflowHub Bot

nf-core/ampliseq

GitHub Actions CI Status GitHub Actions Linting StatusAWS CInf-test ...

Type: Nextflow

Creators: Daniel Straub, Alexander Peltzer

Submitter: WorkflowHub Bot

Assembly-decontamination-VGP9/main

Decontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses NCBI FCS GX to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.

Type: Galaxy

Creators: Delphine Lariviere, Nadolina Brajuka

Submitter: WorkflowHub Bot

nf-core/funcscan

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Jasmin Frangenberg, Anan Ibrahim, James A. Fellows Yates

Submitter: WorkflowHub Bot

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