Workflows

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

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

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

  1. Hifi long reads [fastq]
  2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
  3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
  4. K-mer database [meryldb]
  5. Genome profile summary generated by Genomescope [txt]
  6. Name of first assembly
  7. Name of second assembly ...

Type: Galaxy

Creators: Delphine Lariviere, Galaxy, VGP

Submitter: WorkflowHub Bot

This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.

Type: Galaxy

Creators: Lucille Delisle, Pierre Osteil, Wolfgang Maier

Submitter: WorkflowHub Bot

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

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

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