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Engineering & DevOps for Biology

Pipelines That
Run Themselves.
Built by PhDs.

Custom Nextflow & Snakemake pipelines. Docker containerization. Cloud & on-prem deployment. Monthly maintenance retainers. Written in Python, Rust, Bash, Perl — whatever your stack needs. From $5,000.

Scope Your Pipeline → What We Build
Fully Containerized Tested & Documented You Own the Code

Stop Babysitting Fragile Scripts

Your lab has sequencing data flowing in. Your analysis pipeline is a tangle of bash scripts, hardcoded paths, and one person who knows how it works. We fix that.

✗ What You Have Now

✗Bash scripts with hardcoded paths that break when anything changes
✗One person who "knows" the pipeline — and everyone panics when they're on leave
✗Manual steps between tools — copy files, rename, re-run, check, repeat
✗Different results on different machines — "works on my laptop" syndrome
✗No version tracking, no audit trail, no reproducibility for publications
✗Maxing out your local server while cloud GPUs sit idle

✓ What We Deliver

✓Production-grade Nextflow / Snakemake pipeline — one command, end-to-end
✓Full documentation — anyone on your team can run it, modify it, debug it
✓Docker / Singularity containers — identical results on any machine, every time
✓Automated QC, error handling, notifications — the pipeline manages itself
✓Git-versioned, CI-tested, with sample test datasets — auditable and reproducible
✓Cloud-ready (AWS Batch / GCP Life Sciences) or optimized for your on-prem server
What We Build

Five Pipeline Services

From a single custom pipeline to full infrastructure overhaul with ongoing support.

Custom NGS Pipeline Development

$5K–$20K

End-to-end bioinformatics pipeline built to your exact specifications. RNA-Seq, WGS/WES variant calling, metagenomics, ChIP-Seq, ATAC-Seq, or any custom workflow. Written in Nextflow or Snakemake with Docker containers for every tool.

Nextflow or Snakemake pipeline
Docker/Singularity containers
Config files (params, profiles)
Automated QC & error handling
Sample test dataset + CI tests
User documentation (README + wiki)
1 month of post-delivery support
Git repository (you own it)
Nextflow Snakemake WDL
TAT: 2-4 weeks

Containerization & Reproducibility

$2K–$8K

Already have a working pipeline but it only runs on one machine? We containerize it — every tool, every dependency, every version pinned. Docker for cloud, Singularity for HPC. Includes multi-stage builds, minimal image sizes, and security scanning.

Dockerfiles (multi-stage, optimized)
Singularity definition files
docker-compose for local dev
Container registry setup
Version-pinned dependencies
Reproducibility validation report
DockerSingularity CondaBiocontainers
TAT: 1-2 weeks

Cloud Deployment & Optimization

$5K–$15K

Deploy your pipeline on AWS, GCP, or Azure — with auto-scaling, spot/preemptible instances for cost savings, S3/GCS storage integration, and monitoring. We set up the infrastructure so your pipeline scales from 10 to 10,000 samples without manual intervention.

AWS Batch / GCP Life Sciences setup
Spot instance configuration
S3/GCS storage architecture
IAM roles & security config
Cost monitoring & alerts
Terraform / CloudFormation IaC
AWSGCP Terraform Nextflow Tower
TAT: 2-4 weeks

On-Prem Server Setup

$3K–$10K

Got a Linux server or HPC cluster? We optimize it for bioinformatics workloads — install and configure tools, set up job schedulers (SLURM, PBS), configure storage, tune performance, and deploy your pipelines for maximum throughput.

Linux server hardening
SLURM / PBS scheduler setup
Bioinformatics tool stack install
Storage architecture (NFS/ZFS)
GPU setup for ML / AlphaFold
Performance benchmarking report
Ubuntu CentOS SLURM CUDA
TAT: 1-2 weeks

LIMS & System Integration

$5K–$15K

Connect your bioinformatics pipeline to your LIMS, EHR, or data management system. Auto-trigger analysis when samples arrive, push results back to the database, generate alerts and reports. REST API development, webhook integration, HL7/FHIR for clinical settings.

LIMS ↔ pipeline integration
REST API development
Webhook triggers & listeners
HL7 / FHIR support (clinical)
Database connectors (PostgreSQL, MySQL)
Error notification (Slack, email)
PythonREST FHIR PostgreSQL
TAT: 2-4 weeks

Our Engineering Stack

Full Suite

LANGUAGES

Python Rust Bash Perl Julia R

WORKFLOW ENGINES

Nextflow Snakemake WDL/Cromwell CWL

INFRASTRUCTURE

Docker Singularity AWS GCP Terraform SLURM Git/CI
Recurring Revenue

Monthly Maintenance Retainers

Your pipeline doesn't stop after deployment. Tools update, bugs surface, data formats change. A retainer keeps everything running — and gives you a bioinformatics engineer on call.

Starter

For labs with a stable pipeline needing occasional updates

$2,000/mo

Billed monthly · Cancel anytime

Up to 8 hours/month
Bug fixes & troubleshooting
Tool version updates
Email support (48hr response)
Monthly health check report
Get Started
Most Popular

Growth

For active labs with evolving pipeline needs

$5,000/mo

Billed monthly · 10% off annual

Up to 20 hours/month
Everything in Starter
New feature development
Pipeline extensions & modules
Slack/Teams support (24hr SLA)
Quarterly architecture review
Get Started

Enterprise

For organizations with critical production pipelines

$8,000/mo

Annual contract · Custom SLA

Up to 40 hours/month
Everything in Growth
Dedicated engineer assigned
Same-day emergency response
On-call coverage
Custom SLA & reporting
Contact Us

Project Pricing Summary

Service Starting At Typical Range Timeline Billing
Custom NGS Pipeline $5,000 $5K–$20K 2-4 weeks 50/50 milestone
Containerization $2,000 $2K–$8K 1-2 weeks Fixed price
Cloud Deployment $5,000 $5K–$15K 2-4 weeks 50/50 milestone
On-Prem Server Setup $3,000 $3K–$10K 1-2 weeks Fixed price
LIMS / System Integration $5,000 $5K–$15K 2-4 weeks Milestone-based
Maintenance Retainer $2,000/mo $2K–$8K/mo Ongoing Monthly
Full Infra Overhaul $15,000 $15K–$50K 4-8 weeks Milestone-based
FAQ

Pipeline Questions

Nextflow or Snakemake — which should I choose?

Both are excellent. Nextflow is stronger for cloud-native workflows (AWS Batch, Google Cloud), has better resume/restart, and is the nf-core standard. Snakemake is more popular in academic settings, has a gentler Python-based learning curve, and integrates well with Conda. We recommend Nextflow for production/clinical pipelines and Snakemake for research labs — but we're happy to build in either. We'll recommend the best fit during consultation.

Can you migrate my existing bash scripts to a proper pipeline?

Absolutely — this is one of our most common projects. Send us your existing scripts and we'll audit them, identify the workflow logic, and rebuild everything in Nextflow/Snakemake with containers, proper config management, and documentation. We validate that the new pipeline produces identical results to your original scripts before handoff.

Do I own the code?

Yes — 100%. All code, Dockerfiles, configs, documentation, and tests are delivered in a Git repository that you own. We transfer full IP rights upon final payment. No vendor lock-in. If you stop working with us, your pipeline keeps running.

Can I use the pipeline on our HPC cluster with Singularity?

Yes. Both Nextflow and Snakemake support Singularity natively, and many HPC clusters require it over Docker for security. We build Singularity-compatible containers and test on SLURM/PBS schedulers. We'll include an HPC profile in your pipeline config so it runs with a simple flag change.

What does the retainer include month to month?

Depends on the tier, but typically: bug fixes when something breaks, updating tool versions (e.g. GATK 4.5 → 4.6), adding new reference genomes or annotation databases, performance optimization, responding to your team's questions, and a monthly health check report. Growth and Enterprise tiers include new feature development — adding new analysis modules, new reporting formats, etc. Think of it as having a bioinformatics DevOps engineer on retainer.

Can you build pipelines in Rust or Julia for performance?

Yes — for performance-critical components. While the workflow orchestration layer is Nextflow/Snakemake, individual tools or processing steps can be written in Rust (for speed and memory safety) or Julia (for scientific computing). We've built custom parsers, compression tools, and data processors in Rust that run 10–50x faster than Python equivalents. We recommend this for high-throughput pipelines processing thousands of samples.
Get Started

Tell Us What
You're Building.

Free architecture consultation. We assess your current setup, recommend the right approach, and deliver a clear proposal within 48 hours.

Request Pipeline Consultation

Proposal within 48 hours. No obligation.

Need Analysis Too?

We build pipelines AND run them. Explore our analysis services.

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NGS Data Analysis

From $150/sample
🧬

Protein Modeling & Docking

From $500/target
📋

All Services

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