Workflows

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211 Workflows visible to you, out of a total of 211
dada2/main

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

fluorescence-nuclei-segmentation-and-counting/main

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

assembly-with-flye/main

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

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

velocyto/Velocyto-on10X-from-bundled

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

gromacs-mmgbsa/main

MMGBSA simulation and calculation

Type: Galaxy

Creators: Simon Bray, Simon Bray

Submitter: WorkflowHub Bot

baredsc/baredSC-1d-logNorm

Run baredSC in 1 dimension in logNorm for 1 to N gaussians and combine models.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

openms-metaprosip/main

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Type: Galaxy

Creator: Matthias Bernt

Submitter: WorkflowHub Bot

average-bigwig-between-replicates/main

We assume the identifiers of the input list are like: sample_name_replicateID. The identifiers of the output list will be: sample_name

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

polish-with-long-reads/main

Racon polish with long reads, x4

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

parallel-accession-download/main

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

Type: Galaxy

Creators: Marius van den Beek, IWC

Submitter: WorkflowHub Bot

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