Workflows

What is a Workflow?
834 Workflows visible to you, out of a total of 910
Assembly-Hifi-only-VGP3/main

Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge-duplicates-one-haplotype-VGP6b/main

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5).

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Scaffolding-HiC-VGP8/main

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps. ...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Assembly-Hifi-Trio-phasing-VGP5/main

Generate phased assembly based on PacBio HiFi reads and parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2. This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury plots, and the genome assembly contigs in fasta and GFA format.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

nf-core/airrflow

GitHub Actions CI Status GitHub Actions Linting Status AWS CI ...

Type: Nextflow

Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer

Submitter: WorkflowHub Bot

mags-building/main

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

mfassignr/main

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

qcxms-sdf/main

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

KNIME workflow to gather ChEMBL permeability data
Deprecated
No description specified

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

How Usable Are Published Permeability Data?
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

Powered by
 (v.1.16.0)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH