The 3D'omics code hub is the common space to develop, share and discuss about bioinformatic and statistical code used in 3D'omics. It contains multiple repositories dedicated to specific data processing and analysis steps. 3D'omics deals with two main types of omic data, conventional data generated at the macroscopic level (from faecal samples, gut contents, mucosal scrapes, etc.), and data generated at the micro-scale from intestinal microdissections. The multiple repositories stored in this hub are organised accordingly:

Bioinformatics repositories are snakemake-based pipelines converting raw sequencing files into datasets ready for downstream statistical analyses and visualisations.

• hg_genotype: Host genomics
• ht_quant: Host transcriptomics
• mg_assembly: Microbial genome-resolved metagenomics
• mg_quant: Microbial quantification
• mt_quant: Microbial metatranscriptomics

These repositories are under development.

• Microbial metagenomics
• Microbial metatranscriptomics

Statistics repositories principally contain RMarkdown documents with useful scripts for analysing both macro- and micro-scale multi-omic data.

These repositories are under development.

These repositories are under development.

In 3D'omics we are analysing host genomic and microbial metagenomic data of various animals and their associated microbial communities. Many of the pipelines included in this code hub require the usage of reference animal genomes, for removing host reads, for mapping against protein-coding genes, etc. The reference genomes selected for 3D'omics analyses are the following:

• Reference assembly: https://www.ncbi.nlm.nih.gov/genome/84?genome_assembly_id=317145
• Sequence: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.fna.gz
• Annotations: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.gff.gz

3D'omics is a H2020 project that aims to reconstruct host-microbiota interactions in 3D at the micro-scale through a novel technology. Using poultry and swine production systems, we are analysing the effects of different factors, including animal development, diet, exposure to pathogens, and management practices on the so-called 3D omics landscapes of animal intestines. Further information about the project can be found in the project website.

3D'omics is an ongoing project, and as such, many of the code chunks and pipelines stored in this hub are under development. For that reason, some of the repositories are only accessible for project members. When those repositories contain consolidated contents, we will make them public so that other researchers can also implement the procedures in their research.

This project has received funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement number No. 101000309