Workflows

What is a Workflow?
68 Workflows visible to you, out of a total of 68

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

Assemble long reads with Flye, then view assembly statistics and assembly graph

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

No description specified

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gcms/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

MMGBSA simulation and calculation

Type: Galaxy

Creators: Simon Bray, Simon Bray

Submitter: WorkflowHub Bot

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

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