You almost certainly arrived holding data. Find the row that matches it.

flowchart LR
  I["🧬 Instrument<br/>PacBio · ONT · AVITI · MGI"]
  P["Platform toolkits<br/><i>pacbio-tools · nanopore-tools<br/>aviti-tools · ngs-tools</i>"]
  A["Assay pipelines<br/><i>16S · ITS · exome · shotgun</i>"]
  V["Variants & genomes<br/><i>variant_analysis · ChimericSeq</i>"]
  R["Figures & apps<br/><i>plotting-tools · Shiny-apps</i>"]
  D["📦 Delivery to the researcher"]

  I --> P --> A --> R --> D
  P --> V --> R
  O["Core operations<br/><i>admin-tools · NC_cloud-dl</i>"] -.-> P
  O -.-> A
  O -.-> D

Platform toolkits do the demultiplexing and QC that every project needs. Assay pipelines take it from there. Reporting code is deliberately separate, so the same figures can be regenerated years later.

Each family has its own index with a repo-by-repo breakdown.

Prefer to browse rather than be routed? All repositories on GitHub → — ordered by last push. Note that org-wide maintenance batches (licence and template sweeps) count as pushes, so recent dates there do not always mean recent work.

Our names are a convention, not an accident. Once you know the prefix, you know what you are looking at:

Not every name follows it. Repos that predate the convention (benchmarks, InSilico_PCR, Shiny-apps, variant_analysis, 16S_analysis_pipeline) and forks that keep their upstream name (ChimericSeq, mplotter) are left as they are on purpose — a rename leaves a silent GitHub redirect, so old clones keep working while quietly pointing somewhere else. Use the topic filters below rather than the prefix when you are unsure.

Every repository carries topics on four axes. These are curated, not guessed — filtering on one gives you a real shortlist:

Language topics (bash, python, r, nextflow) are there too, but they describe how it is written rather than what it does.

shotgun and assembly link to a family page rather than a filter: the repos carrying those topics are internal, so the filter would return nothing to a visitor.

A note on what you can see. A good part of the Core's code is internal: LIMS-adjacent web tools, instrument dashboards, pricing calculators, and infrastructure that only makes sense inside our network. Those repos are private and deliberately absent from this page. Everything indexed here is public and usable outside VIB.

Our code is licensed GPL-3.0: use it, adapt it, redistribute it — credit VIB Nucleomics Core and licence derived work under the same terms. Documentation and tutorial repos carry CC BY-SA 4.0 instead, and each repo's LICENSE is authoritative — the few repos forked from upstream projects keep the upstream licence. Everything was relicensed on 2026-08-27 from CC BY-SA 3.0, which no licence scanner could read and which Creative Commons does not recommend for source code; copies obtained before that date remain available under the old terms.

The code is written to be read, mostly Bash and R with comments rather than frameworks. A few caveats before you clone:

• Pipelines assume our reference layout. Paths and reference genome locations are usually configurable at the top of the script; check there first.
• Container images beat manual installs. Where a _docker sibling exists, use it.
• Issues are welcome, including from outside VIB. We read them.

Created and maintained by Stephane Plaisance — VIB Nucleomics Core.

Contributions from the Core's bioinformatics and lab teams across the repos listed above.

_{Org profile v1.2.3 · 2026-08-27 · nucleomics.be}