New lab or startup? We build your scalable computational pipelines.
Production-grade, reproducible omics pipelines on your cloud or cluster, then flat-rate monthly maintenance so they keep working as tools, references and your science change.
In short
OmicsQuest designs and builds bioinformatics pipelines in Nextflow (nf-core) or Snakemake for single-cell, spatial, bulk sequencing, proteomics and imaging data. They run on AWS, Google Cloud, Azure or SLURM. After a fixed-price build, we maintain them for a flat monthly fee starting at $1,490/month, with analysis support from the same duo team. You own all the code.
Signs you need a pipeline, not another script
If any of these sound familiar, every new dataset is costing you more than it should.
Today
- Analysis lives on one person's laptop
- Results from last quarter cannot be reproduced
- QC thresholds change from run to run
- Every new dataset takes weeks of manual work
- Due diligence asks how results were generated, and nobody knows
After we build it
- Versioned, containerized pipelines in your Git repository
- Every figure traces back to inputs, parameters and code
- Automated QC reports for each run
- New data processed in hours, not weeks
- Documentation an auditor, investor or new hire can follow
Build once, then a flat monthly fee
A fixed-price build, then predictable maintenance. No hiring, and no single point of failure.
Pipeline audit
Where you are and what you need.
Free for scoping
- Review of current scripts and data flow
- Recommended architecture and cloud costs
- Fixed-price build proposal
Pipeline build
Production-grade, in 3-8 weeks.
Fixed price, quoted after audit
- Nextflow/nf-core or Snakemake
- Containers (Docker, Apptainer) and pinned references
- Tests on reference data and CI
- Automated QC and MultiQC reports
- Deployment on AWS, GCP, Azure or SLURM
- Documentation and team training
Monthly maintenance
Keep it working, and growing.
$1,490 / month and up
- Tool, reference and security updates
- Run monitoring and bug fixes
- New modules as your assays change
- Reserved analysis hours from your duo team
- Monthly review and cost optimization
What we build pipelines for
Each pipeline follows the best practices described on our service pages.
- Single-cell RNA-seq analysis
- snATAC-seq and scATAC-seq analysis
- Multiome and CITE-seq analysis
- TCR/BCR immune repertoire analysis
- CRISPR screen and Perturb-seq analysis
- Visium HD spatial analysis
- Xenium in situ analysis
- Spatial omics (CosMx, MERSCOPE, GeoMx, CODEX)
- Bulk RNA-seq analysis
- ChIP-seq, CUT&RUN and ATAC-seq
- WGS, WES and variant analysis
- Metagenomics and microbiome
- Proteomics and phosphoproteomics
- Protein-protein interaction (PPI) analysis
- Cell Painting and single-cell phenomics
- Live-cell imaging and cell tracking
- Target discovery (TargetQuest)
- Drug discovery and repurposing
From one of our builds
Pipeline questions
What does the monthly maintenance fee include?
Starting at $1,490/month: tool and reference updates, security patches, monitoring of runs, bug fixes, small new modules, a monthly review, and a reserved block of analysis or support hours. The scope is agreed in writing and the fee is flat.
Do we own the pipeline?
Yes. All code lives in your Git repository and runs on your cloud account or HPC. If you hire in-house later, they inherit a documented, tested codebase.
Which clouds and schedulers do you support?
AWS (Batch, HealthOmics), Google Cloud (Batch), Azure Batch, Seqera Platform, and on-premise SLURM, SGE or LSF clusters.
Nextflow or Snakemake?
We default to Nextflow with nf-core modules for portability and community support, and we build and maintain Snakemake when your team already uses it.
How long does a pipeline build take?
Typically 3-8 weeks, depending on how many data types and how much custom logic you need. The build is quoted as a fixed price after a short audit.
Let us build the pipeline you will rely on.
Send a few lines about your experiment. A bioinformatician and a biologist will review it and reply with questions or a capped estimate. Analysis starts at $79/hour, and figure customization is unlimited.
- Free 30-minute scoping call
- Capped estimate before any billable work
- You own all data, code, figures and IP
Prefer email? contact@omicsquest.com