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HoloRuminant project

HoloR-tools

HoloR-tools is a collection of open-access bioinformatic tools and workflows developed during the HoloRuminant project. They support the analysis of ruminant microbiome data, including associating microbial features with host variables, identifying beneficial microbes and building microbiome networks.

Tools

  • Tool

    NNforge

    Trains an artificial neural network on 16S rRNA gene data to predict genome-scale metabolic models for microbes. It makes metabolic modelling possible from metataxonomic data when metagenomic sequence data is not available.

    Publications and records

    • Øyås et al. 2024 preprint DOI: 10.1101/2024.01.26.576649
      How to cite Øyås et al. 2024

      Øyås, O., Kobel, C. M., Vik, J. O., & Pope, P. B. (2024). Predicting microbial genome-scale metabolic networks directly from 16S rRNA gene sequences. bioRxiv. https://doi.org/10.1101/2024.01.26.576649

    Source repository for NNforge

  • Workflow

    Snakebite-Holoruminant-Meta

    A Snakemake metagenomic pipeline covering read-based analysis, contig-based analysis, and MAG assembly and annotation. It uses a broad set of annotators and public databases, and suits users who do not know every individual tool.

    Publications and records

    • Manuscript in preparation in preparation
    Source repository for Snakebite-Holoruminant-Meta

  • Pipeline

    CompareM2

    A genomes-to-report pipeline for microbial genomics. It analyses assemblies of isolates and metagenomes (MAGs) and produces a report with publication-ready figures.

    Publications and records

    • Kobel et al. 2025 publication DOI: 10.1093/bioinformatics/btaf517
      How to cite Kobel et al. 2025

      Kobel, C. M., Aho, V. T. E., Øyås, O., Nørskov-Lauritsen, N., Woodcroft, B. J., & Pope, P. B. (2025). CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. Bioinformatics, 41(9). https://doi.org/10.1093/bioinformatics/btaf517

    Source repository for CompareM2

  • R package

    FANCY

    An R package that infers association networks. It combines k-nearest neighbour mutual information (via MRNET) and distance correlation into one hybrid edge score. It was designed for MAG co-abundance networks and works with any numeric feature matrix.

    Publications and records

    • Lai et al. 2026 publication DOI: 10.12688/openreseurope.24421.1
      How to cite Lai et al. 2026

      Lai, W., Leu, A., Hvidsten, T. R., Pope, P. B., & Roehe, R. (2026). Nonlinear network inference reveals two independent axes of ecological organisation in the rumen microbiome. Open Research Europe, 6, 381. https://doi.org/10.12688/openreseurope.24421.1

    Source repository for FANCY

  • Tool Coming soon

    CowPI2

    A command line tool for functional prediction from 16S rRNA gene microbiome data. It uses curated, environment-specific HoloRuminant MAG data. Described in Deliverable D1.5.

  • Web app

    Clann Tree Viewer

    An interactive viewer for phylogenetic trees in Newick, NEXUS and NHX formats, including Clann reconciliations. It runs entirely in the browser and no data leave the user's computer. Designed mainly for teaching.

    Developed by
    Chris Creevey

    Publications and records

    • Zenodo record software DOI: 10.5281/zenodo.22871890
      How to cite Zenodo record

      Creevey, C. (2026). ChrisCreevey/clann-tree-viewer: V1.1 (Version V1.1) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22871890

    Open app for Clann Tree Viewer Source repository for Clann Tree Viewer

  • Web app

    Clann BLAST Explorer

    An explorer for BLAST (-outfmt 6/7) and DIAMOND tabular output. It provides hit tables, HSP coverage diagrams, taxonomy assignment, reciprocal best hit analysis and FASTA export. All analysis runs in the browser with no data upload.

    Developed by
    Chris Creevey

    Publications and records

    • Zenodo record software DOI: 10.5281/zenodo.22871507
      How to cite Zenodo record

      Creevey, C. (2026). ChrisCreevey/clann-blast-explorer: Version 1 - First Release (Version V1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22871507

    Open app for Clann BLAST Explorer Source repository for Clann BLAST Explorer

  • Web app

    Clann Pangenome Explorer

    Joins pangenome matrices from Roary, Panaroo, PIRATE or PanACoTA with gene annotations and CoinFinder results. It summarises core and accessory genome structure, tags AMR or virulence genes and visualises association networks. All analysis runs in the browser.

    Developed by
    Chris Creevey

    Publications and records

    • Zenodo record software DOI: 10.5281/zenodo.22871457
      How to cite Zenodo record

      Creevey, C. (2026). ChrisCreevey/clann-pangenome-explorer: Version 1 - Frist Release (Version V1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22871457

    Open app for Clann Pangenome Explorer Source repository for Clann Pangenome Explorer

  • Web app

    Clann eDNA Explorer

    An explorer for taxonomic classification results from eDNA metabarcoding and metagenomic studies. It accepts Kraken2/Bracken, QIIME 2 and lineage tables, and produces sunburst and Sankey diagrams, heatmaps, diversity indices and similarity measures. All processing runs in the browser.

    Developed by
    Chris Creevey

    Publications and records

    • Zenodo record software DOI: 10.5281/zenodo.22662075
      How to cite Zenodo record

      Creevey, C. (2026). ChrisCreevey/clann-edna-explorer: V1.0 - Initial release (Version V1.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22662075

    Open app for Clann eDNA Explorer Source repository for Clann eDNA Explorer