Workflows

What is a Workflow?
1197 Workflows visible to you, out of a total of 1281

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

Type: Python

Creator: Zhi Song

Submitter: Zhi Song

DOI: 10.48546/workflowhub.workflow.1305.1

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, ...

Type: Galaxy

Creators: Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler, Santino Faack

Submitter: WorkflowHub Bot

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

Type: Galaxy

Creators: Kristina Gomoryova, Helge Hecht, RECETOX, MUNI

Submitter: WorkflowHub Bot

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.

Type: Galaxy

Creators: Helge Hecht, RECETOX

Submitter: WorkflowHub Bot

Deprecated
No description specified

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

Deprecated

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

Stable

High-Performance Computing (HPC) environments are integral to quantum chemistry and computationally intense research, yet their complexity poses challenges for non-HPC experts. Navigating these environments proves challenging for researchers lacking extensive computational knowledge, hindering efficient use of domain specific research software. The prediction of mass spectra for in silico annotation is therefore inaccessible for many wet lab scientists. Our main goal is to facilitate non-experts ...

Type: Galaxy

Creators: Zargham Ahmad, Helge Hecht, Wudmir Rojas, RECETOX SpecDat

Submitters: Helge Hecht, Wudmir Rojas

DOI: 10.48546/workflowhub.workflow.897.3

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Chelsea Sawyer, Edmund Miller, Matthias De Smet

Submitter: WorkflowHub Bot

Barcode Gene Extractor & Evaluator (BGEE) Snakemake workflow

Snakemake workflow for recovering high-quality barcode sequences from genome skim data, built around MitoGeneExtractor and adapted for genome skims of museum specimens.

Contents

Type: Snakemake

Creator: Dan Parsons

Submitter: Dan Parsons

Stable

Laserfarm (https://doi.org/10.1016/j.ecoinf.2022.101836) is a high-throughput workflow for generating geospatial data products of ecosystem structure using LiDAR point clouds from national or regional airborne laser scanning (ALS) surveys. The workflow example here shows the application of the Laserfarm workflow to the 7.5 km2 large Reserve Naturelle Nationale du Bagnas ('Bagnas') in France (3.514360 E, 43.314332 N). The work has been performed in the context of the EU project MAMBO (Modern ...

Type: Jupyter

Creators: W. Daniel Kissling, Wessel Mulder, Jinhu Wang, Yifang Shi

Submitter: W. Daniel Kissling

DOI: 10.48546/workflowhub.workflow.1297.1

Powered by
(v.1.17.0-main)
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH