Workflows

workflow-automation

Associated Tutorial

This workflows is part of the tutorial Automating Galaxy workflows using the command line, available in the GTN

Thanks to...

Workflow Author(s): Wolfgang Maier

Tutorial Author(s): Simon Bray, [Wolfgang ...

Associated Tutorial

This workflows is part of the tutorial Multiomics data analysis using MultiGSEA, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

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

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

This workflow was built for the 2024 Bioinformatics Bootcamp at The Open University. It is meant to occur after the (universal) Filter, plot and explore tutorial to allow analysis of a single cluster.

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

This workflow was developed for the 2024 Bioinformatics Bootcamp at The Open University. It imports datasets from the EBI SCXA, reformats then, and analyses them similar to the Filter, plot and explore Galaxy tutorial.

This workflow constructs Metagenome-Assembled Genomes (MAGs) using SPAdes or MEGAHIT as assemblers, followed by binning with four different tools and refinement using Binette. The resulting MAGs are dereplicated across the entire input sample set, then annotated and evaluated for quality. You can provide pooled reads (for co-assembly/binning), individual read sets, or a combination of both. The input samples must consist of the original reads, which are used for abundance estimation. In all cases, ...

This workflow can be used to assign multi-element molecular formulas to ultrahigh resolution mass spectra.

Workflow to predict EI mass spectra using QCxMS starting from a single SDF file, containing the 3D coordinates of all atoms in the molecule. These files can typically be obtained from PubChem.