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Pipelines

From reads to results,
automatically

Every Omicsy pipeline is cloud-executed, version-controlled, and reproducible — data in, results out, no environment setup. Genome-resolved metagenomics is live today, with more omics workflows on the way.

Available now Metagenomics

Genome-resolved metagenomics

Reconstruct individual genomes from the mixed DNA of whole microbial communities — so you can study who is present and how communities change across samples. The full workflow runs end-to-end on Omicsy today, producing genomes, abundance profiles, and a reproducible record of every step.

  • Quality filtering & assembly. Raw reads are cleaned, then assembled into contigs.
  • Binning & dereplication. Contigs are grouped into genomes and reduced to a non-redundant set.
  • Mapping & taxonomy. Reads are mapped back to quantify abundance, and genomes are placed taxonomically.
Run it now
QC Assembly Binning Mapping Taxonomy
On the roadmap What's next

More omics, coming soon

Genome-resolved metagenomics is the first of many. We are extending the same cloud-executed, reproducible foundation across the omics landscape — each new pipeline validated and documented before it ships.

  • Metagenomics, expanded. Amplicon microbiome profiling for rapid community surveys.
  • Genomics & transcriptomics. RNA-seq, whole-genome variant calling, and single-cell.
  • Beyond DNA. Epigenomics, proteomics, and metabolomics workflows to follow.
Microbiome profilingsoon RNA sequencingsoon Single-cellsoon Whole-genome sequencingsoon Epigenomicssoon Proteomics & metabolomicssoon
Bespoke

Need a specific pipeline?

The roadmap is not a waiting list. If your work depends on a workflow we have not shipped yet, tell us — user-requested pipelines can be implemented on the same reproducible, cloud-native foundation and made available in your workspace.

  • Propose your workflow. Share the tools, inputs, and outputs your analysis needs.
  • We scope and build it. Versioned and validated like every Omicsy pipeline.
  • Runs like any other. Point, click, and run — with full provenance and reproducibility.
Request a pipeline
your workflow we build your pipeline
Ready when you are

Run your first
pipeline

Create a workspace, bring in your reads, and launch genome-resolved metagenomics in minutes — no setup, no code, free to begin.

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Genome-resolved metagenomics, live now · Read the docs