Workflows

What is a Workflow?
230 Workflows visible to you, out of a total of 246

Structural and functional genome annotation with Funannotate

Type: Galaxy

Creator: Anthony Bretaudeau

Submitter: Paul De Geest

Masking repeats in a genome using RepeatMasker

Type: Galaxy

Creator: Anthony Bretaudeau

Submitter: Paul De Geest

EBP-Nor Genome Assembly pipeline

This repository contains the EBP-Nor genome assembly pipeline. This pipeline is implemented in snakemake. This pipeline is developed to create haplotype-resolved genome assemblies from PacBio HiFi reads and HiC reads, and is primarly designed for diploid eukaryotic organisms. The pipeline is designed to work on a linux cluster with slurm as workload manager.

Requirements & Setup

Some software need to be configured/installed before the pipeline can be run ...

Type: Snakemake

Creators: None

Submitter: Bram Danneels

Workflow for Creating a large disease network from various datasets and databases for IBM, and applying the active subnetwork identification method MOGAMUN.

Type: Common Workflow Language

Creators: Daphne Wijnbergen, Mridul Johari

Submitter: Daphne Wijnbergen

DOI: 10.48546/workflowhub.workflow.681.7

Type: COMPSs

Creator: Joser Carbonel

Submitter: Miguel Vazquez

Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment

Introduction

Phylogeny refers to the evolutionary history and relationship between biological lineages related by common descent. Reticulate evolution refers to the origination of lineages through the complete or partial merging of ancestor lineages. Networks may be used to represent lineage independence events in non-treelike phylogenetic processes.

The methodology for reconstructing networks ...

Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data

Hall, M, Coin, L., Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data. bioRxiv 2023. doi: [10.1101/2023.09.18.558339][doi]

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and classification of M. tuberculosis reads.

This repository contains the code and ...

Type: Snakemake

Creator: Michael Hall

Submitter: Michael Hall

DOI: 10.48546/workflowhub.workflow.700.2

BACPAGE

This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology. Read the complete documentation and instructions for bacpage and each of its functions here

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools ...

Type: Workflow Description Language

Creators: None

Submitter: Nathaniel Matteson

Work-in-progress

bacpage{width=500}

This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology.

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools have been developed to analyze this data, but very few tools ...

Type: Workflow Description Language

Creators: None

Submitter: Nathaniel Matteson

Stable

Snakemake workflow: dna-seq-varlociraptor

Snakemake GitHub actions status DOI

A ...

Type: Snakemake

Creators: Felix Mölder, David Lähnemann, Johannes Köster

Submitter: Johannes Köster

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