Resources / open science
Here you can use the databases, software and step-by-step analyses we have produced through our research and collaborations.
Access · reuse · reproduce
Open data
Search, browse and download multi-omic datasets generated by our international research collaborations.
Animal production
Explore chicken and salmon samples, analysis summaries, genome catalogues, viral catalogues and API access from the HoloFood project.
Spatial multi-omics
Discover conventional and microscale multi-omic data generated to reconstruct host–microbiota interactions in three dimensions.
Global hologenomics
Find specimens, hologenomes and metagenome-assembled genomes collected through the Earth Hologenome Initiative.
Open-source software
Reusable packages and command-line tools for accessing, analysing and comparing complex biological data.
Command line · Python API
Find, summarise, export and download records from the 3D’omics data catalogue. 3dtk works from the command line or Python, needs no credentials or server, and verifies its published catalogue before use.
Install
pip install 3dtk
Then run 3dtk, or import py3dtk in Python.
Command line · Python API
Query, summarise, export and download EHI specimens, hologenomes and metagenome-assembled genomes. EHItk includes a versioned SQLite catalogue for reproducible command-line and Python workflows.
Install
pip install ehitk
Then run ehitk --help, or import ehitk in Python.
R package
Measure and compare biological communities through one framework for neutral, phylogenetic and functional Hill diversity, including partitioning, dissimilarity, profiles, evenness and redundancy.
Install
devtools::install_github("alberdilab/hilldiv3")
Load the package with library(hilldiv3).
Command line
Map paired shotgun reads to taxonomically annotated COI and ITS reference sequences. BarcodeMapper filters reads with fastp, aligns them with Bowtie2, and assigns each read to the lowest taxonomy shared by its accepted alignments, producing a taxonomy count table, an HTML report and a run manifest.
Install
python -m pip install --no-deps <release wheel>
Then run barcodemapper --build and barcodemapper -i reads.
Mac app
One Mac app that brings a code editor, terminals, an agent chat coordinating Claude Code and Codex, Slurm jobs, file transfer, report previews, Git/GitHub, Zenodo and PyPI into a single window.
Install
git clone https://github.com/anttonalberdi/codeome.git
Then run npm install and npm run dist.
Reproducible research
Paper-specific webbooks expose the code and analytical decisions behind published results.
A reproducible walkthrough of the diversity, community-composition and functional analyses behind the study.
Code and analysis for a global genome-resolved comparison of domestic and feral cat gut microbiomes.