This is an inclusive collection of workflows related to biodiversity and ecology (especially non-microbial). A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). It also aims at collating workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and regardless of the workflow format (Galaxy, Nextflow, Snakemake, etc.).
This collection focuses on wildlife; and genomics, ecology, biogeography, and evolution of wildlife across all kingdoms of life on Earth, especially "macroscopic". The focus of this collection is on multicellular, "macroscopic" eukaryotes, because there is an abundance of other tools and services working with microorganisms and their ecology.
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ERGA DataQC HiFi v2505 (WF0)
from "ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)" - Added 21 days ago -
ERGA DataQC ONT v2505 (WF0)
from "ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)" - Added 21 days ago -
ERGA DataQC Illumina v2505 (WF0)
from "ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)" - Added 21 days ago -
ERGA Profiling Long Reads v2505 (WF1)
from "ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)" - Added 21 days ago -
ERGA Long reads-only Assembly+QC Hifiasm v2505 (WF2)
from "ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)" - Added 21 days ago -
ERGA Long Reads PriAlt Purge+QC v2505 (WF3)
from "ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)" - Added 21 days ago -
ERGA HiC Pri Scaffolding+QC YaHS v2505 (WF4)
from "ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)" - Added 21 days ago -
CLAWS (CNAG's long-read assembly workflow in Snakemake)
one of the genomes assembly workflows used by Biodiversity Genomics Europe - Added 21 days ago -
Post-assembly workflow
part of the tutorial ERGA post-assembly QC, available in the GTN - Added 21 days ago -
ANNOTATO - ERGA Genome Annotation Workflow in Nextflow
- Added 21 days ago -
ERGA Protein-coding gene annotation workflow
- Added 21 days ago -
AnnoAudit - Annotation Auditor
evaluating the quality of genomic annotations through a multifaceted approach - Added 21 days ago -
ERGA-BGE Genome Report ASM analyses (one-asm HiFi + HiC)
from "Genome Evaluation for ERGA-BGE Reports" - Added 21 days ago -
ERGA-BGE Genome Report ASM analyses (one-asm WGS Illumina PE + HiC)
from "Genome Evaluation for ERGA-BGE Reports" - Added 21 days ago -
ERGA-BGE Genome Report ANNOT analyses
from "Genome Evaluation for ERGA-BGE Reports" - Added 21 days ago -
HiC scaffolding pipeline
from "ERGA Assembly Snakemake HiFi & HiC Pipelines" - Added 21 days ago -
Purge retained haplotypes using Purge-Dups
from "ERGA Assembly Snakemake HiFi & HiC Pipelines" - Added 21 days ago -
HiC contact map generation
from "ERGA Assembly Snakemake HiFi & HiC Pipelines" - Added 21 days ago -
A workflow for marine Genomic Observatories data analysis
metaGOflow - Added 21 days ago -
skim2mito
a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low-coverage genome skims (designed for museum collections, but works with recently collected samples, too) - Added 21 days ago -
Population and community metrics calculation from Biodiversity data
workflow to calculate species presence/absence, community metrics, and compute generalised linear models to identify effects and their significance to biodiversity - Added 21 days ago -
FAIR data pipeline for marine acoustic data
- Added 21 days ago -
Barcode Gene Extractor & Evaluator (BGEE) Snakemake workflow
workflow for recovering high-quality barcode sequences from genome skims of museum specimens, using MitoGeneExtractor - Added 21 days ago -
Marine Omics identifying biosynthetic gene clusters
- Added 21 days ago -
nf-core/eager
a reproducible and state-of-the-art pipeline for the analysis of ancient DNA - Added 21 days ago -
Calculating and visualizing OBIS marine biodiversity indicators
- Added 21 days ago -
Laserfarm Jupyter Notebooks for Reserve Naturelle Nationale du Bagnas
Laserfarm - a workflow for generating geospatial data of ecosystem structure using LiDAR point clouds from airborne laser scanning (ALS) surveys - applied to European demonstration sites (here Bagnas) - Added 21 days ago -
SPIPOLL MMOS GAPARS crowdsourcing results
workflow for analysing crowdsourcing results of the SPIPOLL hoverflies GAPARS European project - Added 21 days ago

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Created: 30th Jun 2025 at 11:16
Last updated: 10th Jul 2025 at 12:38
