This is a general team for the BGE project for any members affiliated directly or indirectly with the BGE project.

To request joining this team, make sure sure your WorkflowHub institution matches one of the listed BGE partners.

A collection of workflows and pipelines developed as part of the ERGA consortium

A collection of workflows designed to annotate elements of the genome. These include repeat regions, protein-coding genes, ncRNA, miRNA.

HiC scaffolding pipeline

Snakemake pipeline for scaffolding of a genome using HiC reads using yahs.

Prerequisites

This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:

snakemake --use-conda --cores N

where N is number of cores to use. There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring the cluster.json file run:

./run_cluster ...

Purge dups

This snakemake pipeline is designed to be run using as input a contig-level genome and pacbio reads. This pipeline has been tested with snakemake v7.32.4. Raw long-read sequencing files and the input contig genome assembly must be given in the config.yaml file. To execute the workflow run:

snakemake --use-conda --cores N

Or configure the cluster.json and run using the ./run_cluster command

HiC contact map generation

Snakemake pipeline for the generation of .pretext and .mcool files for visualisation of HiC contact maps with the softwares PretextView and HiGlass, respectively.

Prerequisites

This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:

snakemake --use-conda

There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring ...

ANNOTATO - Annotation workflow To Annotate Them Oll

• ANNOTATO - Annotation workflow To Annotate Them Oll
• Overview of the workflow
• Input data
• Pipeline steps
• Output data
• Prerequisites
• Installation
• Running ANNOTATO
• Before running the pipeline (IMPORTANT) ...

ERGA Protein-coding gene annotation workflow.

Adapted from the work of Sagane Joye:

https://github.com/sdind/genome_annotation_workflow

Prerequisites

The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.

conda v 23.7.3 ...

Pipelines used by the genomes assembly teams part of the Biodiversity Genomics Europe project

https://biodiversitygenomics.eu/

Collection of workflows designed to assembled a set of PacBio HiFi and Illumina HiC reads into a chromosome-scale de-novo assembly.

Development versions of these pipelines can be found in the ERGA github and any questions or queries can be raised on the ERGA Discussions Channel

Want to find out more about the work done by ERGA? Become a member ...

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads

Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses

Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4