Workflows

What is a Workflow?
230 Workflows visible to you, out of a total of 246
Work-in-progress

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada. Doi: 10.3389/fmicb.2020.00549

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

No description specified

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Stable

gene2phylo

gene2phylo is a snakemake pipeline for batch phylogenetic analysis of a given set of input genes.

Contents

Setup

The pipeline is written in Snakemake and uses conda to install the necessary tools.

It is strongly recommended to install conda using Mambaforge. See details here ...

Type: Unrecognized workflow type

Creators: None

Submitter: Oliver White

Stable

skim2rrna

skim2rrna is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of ribosomal genes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

Type: Snakemake

Creators: None

Submitter: Oliver White

Stable

skim2mt

skim2mt is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

Type: Snakemake

Creators: None

Submitter: Oliver White

Stable

score-assemblies

A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.

The workflow includes the following programs:

...

Type: Snakemake

Creator: Peter Menzel

Submitter: Peter Menzel

DOI: 10.48546/workflowhub.workflow.786.1

Stable

ont-assembly-snake

A Snakemake wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data, using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.

Included programs

read filtering assembly long read polishing short read polishing reference-based polishing
Filtlong
...

Type: Snakemake

Creator: Peter Menzel

Submitter: Peter Menzel

DOI: 10.48546/workflowhub.workflow.787.1

Work-in-progress

This project is about the automated quantification of wound healing in high-throughput microscopy scratch assays.

Type: Galaxy

Creator: Christian Tischer

Submitter: Yi Sun

Stable
No description specified

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with flavivirus helicases in the Apo or unbound state. The associated input files can be found at: https://zenodo.org/records/7493015 The associated output files can be found at: https://zenodo.org/records/7850935

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