This is a Galaxy workflow for performing molecular dynamics simulations and analysis with coronavirus helicases in the Apo or unbound state. The associated input files can be found at: https://zenodo.org/records/7492987. The associated output files can be found at: https://zenodo.org/records/7851000.

This is a Galaxy workflow for performing molecular dynamics simulations and analysis with flavivirus helicases bound to a ligand/drug molecule. 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

Protype demonstrator of a workflow reducing HESS and INTEGRAL/SPI-ACS data to common Light Curve format and combining the lightcurves into a multi-wavelength observation.

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 ...

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

Cancer Invasion Workflow

Table of Contents

• Cancer Invasion Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• Local machine
• Requirements
• Usage steps
• MareNostrum 4
• [Requirements in ...

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 ...

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 ...

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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 ...