Repositories

The complete list of repositories is available on GitHub.

Find below a selection organised by themes:

Ensembl Compara

muffato/docker-ensembl-linuxbrew-compara: Docker image with all dependencies to run the Ensembl Compara pipelines
Last contribution: 2021-01
muffato/docker-ensembl-linuxbrew-basic-dependencies: Docker image with the basic dependencies for the Ensembl linuxbrew installation
Last contribution: 2021-01
Ensembl/ensembl-compara: The Ensembl Compara Perl API and SQL schema
Last contribution: 2020-12
Ensembl/treebest: TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
Last contribution: 2019-06
muffato/pyEnsemblRest: Python wrapper of the Ensembl REST API
Last contribution: 2019-06

Ensembl/ensembl-hive: EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource
Last contribution: 2020-12
Ensembl/ensembl-hive-slurm: Slurm Meadow for Ensembl Hive
Last contribution: 2020-11
Ensembl/ensembl-hive-docker-swarm: ‘Docker Swarm’ implementation of Ensembl Hive Meadow interface
Last contribution: 2020-03
Ensembl/guiHive: Graphical interface for the eHive workflow manager
Last contribution: 2019-08
Ensembl/ensembl-hive-sge: SGE Meadow for Ensembl Hive
Last contribution: 2018-08
Ensembl/ensembl-hive-htcondor: HTCondor Meadow for Ensembl Hive
Last contribution: 2018-05
Ensembl/ensembl-hive-pbspro: ‘PBS Pro’ implementation of Ensembl Hive Meadow interface
Last contribution: 2018-03
Ensembl/XML-To-Blockly: Takes RelaxNG schema as input and generates corresponding code for a Blockly block to represent the same
Last contribution: 2017-06
muffato/eHive-Blockly: Playground for Blockly and eHive
Last contribution: 2016-10

sanger-tol/nf-core-modules: Repository to host Tree of Life’s Nextflow DSL2 modules
Last contribution: 2026-01
sanger-tol/readmapping: Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.
Last contribution: 2025-12
sanger-tol/genomenote: Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.
Last contribution: 2025-12
sanger-tol/variantcalling: Nextflow DSL2 pipeline to call variants on long read alignment.
Last contribution: 2025-12
sanger-tol/blobtoolkit: Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.
Last contribution: 2025-12
sanger-tol/ensemblrepeatdownload: Nextflow DSL2 pipeline to download repeat annotations from Ensembl.
Last contribution: 2025-12
sanger-tol/sequencecomposition: Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition
Last contribution: 2025-12
sanger-tol/variantcomposition: Nextflow DSL2 pipeline to analyse variants.
Last contribution: 2025-12
sanger-tol/ensemblgenedownload: Nextflow DSL2 pipeline to download gene annotations from Ensembl.
Last contribution: 2025-12
sanger-tol/insdcdownload: Nextflow DSL2 pipeline to download assemblies from INSDC.
Last contribution: 2025-12

nf-core/modules-template: Last contribution: 2026-01
nf-core/nft-utils: nf-test utility functions
Last contribution: 2025-12
nf-core/tools: Python package with helper tools for the nf-core community.
Last contribution: 2025-11
nf-core/modules: Repository to host tool-specific module files for the Nextflow DSL2 community!
Last contribution: 2025-10

singularityhub/singularity-hpc: Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.
Last contribution: 2025-04

DyogenIBENS/Agora: Algorithm For Gene Order Reconstruction in Ancestors
Last contribution: 2024-11
DyogenIBENS/LibsDyogen: Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications
Last contribution: 2022-01
muffato/ensembl-download-java: Java code to download genomes and orthologues from Ensembl
Last contribution: 2011-01
muffato/pywaltrap: Python interface for the community detection program Walktrap
Last contribution: 2011-01
muffato/phd-thesis-scripts: Backup of the scripts I used during my PhD thesis to build the Agora ancestral-genome reconstruction toolkit
Last contribution: 2010-11