Workflows

What is a Workflow?
65 Workflows visible to you, out of a total of 65

Pathogens of all samples report generation and visualization

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1060.1

Microbiome - Taxonomy Profiling

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1059.1

Generate Nx and Size plot for multiple assemblies

Inputs

Collection of fasta files. The name of each item in the collection will be used as label for the Nx and Size plots.

Outputs

  1. Nx plot
  2. Size plot

Type: Galaxy

Creators: Delphine Lariviere, VGP

Submitter: WorkflowHub Bot

This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

Antimicrobial resistance gene detection from assembled bacterial genomes

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

Importing single-end multiplexed data (not demultiplexed yet)

Type: Galaxy

Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ

Submitter: WorkflowHub Bot

Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.

Type: Galaxy

Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ

Submitter: WorkflowHub Bot

dada2 amplicon analysis for paired end data

The workflow has three main outputs:

  • the sequence table (output of makeSequenceTable)
  • the taxonomy (output of assignTaxonomy)
  • the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)

Type: Galaxy

Creators: Matthias Bernt, UFZ Leipzig

Submitter: WorkflowHub Bot

This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html

Type: Galaxy

Creator: Leonid Kostrykin

Submitter: WorkflowHub Bot

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