Workflows

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595 Workflows visible to you, out of a total of 639
VGP hybrid scaffolding with Bionano optical maps

Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP purge assembly with purge_dups pipeline
Work-in-progress

Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP HiFi phased assembly with hifiasm and HiC data
Work-in-progress

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP genome profile analysis
Work-in-progress

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

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

(old) SARS-COV2 version of the V-Pipe workflow

A version of V-pipe (analysis of next generation sequencing (NGS) data from viral pathogens) specifically adapted to analyze high-throughput sequencing data of SARS-CoV-2.

Type: Snakemake

Creators: Ivan Topolsky, Susana Posada Céspedes, Niko Beerenwinkel,

Submitter: Hervé Ménager

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eQTL-Catalogue/qtlmap

eQTL-Catalogue/qtlmap

Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue

Introduction

eQTL-Catalogue/qtlmap is a bioinformatics analysis pipeline used for QTL Analysis.

The workflow takes phenotype count matrix (normalized and quality controlled) and genotype data as input, and finds associations between them with the help of sample metadata and phenotype metadata files (See Input formats and preparation for required input ...

Type: Nextflow

Creators: None

Submitter: Kaur Alasoo

Galaxy Protein Ligand Complex MD Setup
Stable

Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)

This workflow must be run in biobb.usegalaxy.es. Please, click here to access.

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by ...

Type: Galaxy

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.295.3

Python CNS/XPLOR MD Automatic Ligand Parameterization tutorial
Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.293.2

Python Amber Automatic Ligand Parameterization tutorial
Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.292.2

Python GMX OPLS/AA Automatic Ligand Parameterization tutorial
Stable

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.291.2

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