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There is no single “cloud genomics” price
A cloud genomics bill is the sum of several activities rather than a license fee. A small panel analysis that runs once and keeps only a VCF may cost very differently from a whole-genome pipeline that retains FASTQ, BAM or CRAM files, intermediate results and logs for years. Two laboratories can use the same vendor and receive different totals because they choose different regions, storage tiers, workflow resources, retry policies and download patterns.
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Vendor list prices are useful for building an estimate, but they are not a universal industry average. No independent, general-purpose statistic establishes one typical cloud-genomics software price. Treat the figures below as published examples and allowances, then confirm the current calculator, regional price sheet or contract quote for your workload.
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Workflow compute
Variant calling, alignment, quality control, RNA-seq quantification and other jobs consume virtual CPUs, memory, accelerators or specialized instances. Some services meter the resources you request; others package a complete analysis as a per-run charge. Runtime alone is not enough to estimate cost: an over-sized machine, parallel tasks, failed attempts and retries all increase consumption.
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Run file systems and temporary space
Workflows often need a high-performance file system while jobs are running. AWS HealthOmics private workflows charge for requested compute and run file-system resources. Temporary space can therefore add a material line item even when final files are moved to cheaper storage afterward.
Persistent sequence, variant and annotation storage
Raw reads and derived results remain in storage after a run. HealthOmics distinguishes sequence storage from variant and annotation stores and offers active and archive tiers. Google Cloud Healthcare API also separates storage from operations. Illumina includes an account allowance but bills storage beyond that allowance on eligible plans.
Requests, queries and data processing
APIs, metadata operations, ETL jobs, de-identification, database queries and repeated object listings can be charged independently of stored bytes. Google Cloud Healthcare API explicitly includes requests, ETL and de-identification among its billable dimensions.
Data transfer and egress
Uploading data, moving it between services and downloading results can create network charges. Repeatedly exporting large BAM, CRAM or FASTQ files to local infrastructure may cost more than a single analysis run, especially when data is retained in one region and processed or downloaded from another.
Application and platform credits
BaseSpace Sequence Hub expresses storage, compute and third-party application usage in iCredits. An iCredit is a usage unit, not a universal dollar amount; the number needed depends on the application and sample type, while the commercial value depends on the account terms in effect.
AWS HealthOmics pricing model
AWS says HealthOmics supports WDL, Nextflow and CWL workflows and can scale to “tens of thousands of tests per day.” Those are vendor statements, not independent performance guarantees. AWS also states that customers “only pay for what you use and there are no HealthOmics licensing costs.” The practical implication is that you budget metered resources rather than a conventional software subscription.
Private workflows
Private workflows are priced from the compute and run file-system resources you request. A pipeline that uses more memory, more parallel tasks or a longer-lived run file system consumes more billable capacity. Include expected retries and concurrent samples in the estimate; otherwise a nominal per-sample figure will be understated.
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Ready2Run workflows
Ready2Run workflows use a fixed cost per run. This can make a validated, standardized analysis easier to budget than a fully custom pipeline, but the fixed price still needs to be checked for the specific workflow and region. Do not assume that a Ready2Run charge includes long-term storage or downstream data transfer unless the price description says so.
HealthOmics data stores
Sequence, variant and annotation stores have their own storage and tier pricing. Active and archive choices matter: archive storage is generally intended for infrequently accessed data, while active storage is designed for ongoing analysis. Before moving files to an archive tier, check retrieval charges, minimum retention periods and restore time in the current AWS documentation.
New-customer free tier example
AWS lists a HealthOmics new-customer offer for the first two months that includes:
- 275 omics.m.xlarge instance-hours.
- 49,000 GB-hours of run storage.
- 1,500 gigabase-months of active sequence storage.
- 1,500 gigabase-months of archive sequence storage.
- 200 gigabyte-months of variant-store storage.
These are one-time allowance quantities for eligible new customers, not a recurring annual entitlement. Confirm eligibility, expiration and regional availability before using the allowance in a production budget.
Google Cloud Healthcare API pricing model
Google Cloud Healthcare API combines several billing dimensions. Storage is only one part of the bill; requests, ETL, de-identification and network utilization can also contribute. A genomics data service built around the API should therefore be estimated from both the volume of data and the operations performed on it.
Published Iowa storage examples
Google lists structured storage in Iowa at $0.000328767 per GiB-hour for more than 1 GiB through 1,024 GiB. It lists blob storage above 1 GiB at $0.000027397 per GiB-hour. These are regional list-price examples for the stated ranges, not global prices or a complete genomics-workflow quote. Larger volumes, other regions, operations and network use can change the total.
Why API-heavy designs need a separate estimate
Applications that repeatedly query metadata, transform records, de-identify data or move objects between services may generate substantial operation and network usage even when the stored dataset is unchanged. Count expected requests and processing jobs alongside FASTQ, BAM, CRAM and VCF capacity. A storage-only calculation is not sufficient for an API-centered architecture.
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Illumina BaseSpace Sequence Hub and BioInsight credits
Illumina’s billing documentation states that “BaseSpace Sequence Hub storage, compute, and third-party app costs are charged in iCredits.” This sample-oriented system gives you a planning unit, but you must still know how many samples, which application and how much retained storage your account will use.
Published BaseSpace analysis examples
| Analysis or sample type | Published usage | Qualification |
|---|---|---|
| 30× human whole genome | 7 iCredits | Illumina’s sample-oriented example |
| Exome | 2 iCredits | Illumina’s sample-oriented example |
| Cancer panel | 2 iCredits | Illumina’s sample-oriented example |
| Transcriptome | 2 iCredits | Illumina’s sample-oriented example |
| Differential expression | 1 iCredit | Illumina’s sample-oriented example |
| RNA panel | 2 iCredits | Illumina’s sample-oriented example |
| 16S metagenomics | 1–2 iCredits | Illumina’s sample-oriented example |
The table describes analysis consumption, not the final currency price of an account. Multiply the applicable credit requirement by your sample count, then add storage and any other account charges.
Trial and included storage
A BaseSpace trial provides 250 iCredits that expire after 30 days. BaseSpace accounts include a 1 TB storage allowance. Professional and Enterprise accounts are invoiced monthly for storage above 1 TB. The allowance and trial are useful for evaluation, but neither should be treated as an indefinite free tier.
Illumina BioInsight Platform storage
Illumina BioInsight Platform Core lists standard storage at 22.50 BIC/TB/month and archive storage at 2.00 BIC/TB/month. These are BioInsight credits (BIC) and should not be confused with BaseSpace iCredits. Verify the plan, region, currency conversion and any minimums before comparing BIC figures with another vendor’s price.
What does it cost to analyze a whole genome?
There is no defensible single dollar answer without the workflow and account details. A “whole genome” may mean a 30× human dataset aligned and variant-called once, or it may include joint calling across a cohort, quality-control reruns, annotation, long-term retention and repeated exports. The published BaseSpace example assigns 7 iCredits to a 30× human whole genome analysis, but Illumina’s credit-to-currency terms and your storage and transfer usage determine the bill.
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For AWS or Google Cloud, estimate the resource profile rather than multiplying a generic genome price. Record the requested CPU and memory, expected runtime, temporary file-system size, number of samples processed concurrently, retries, retained FASTQ/BAM/CRAM/VCF volume, API operations and data downloaded. Only then apply regional prices, free-tier quantities, committed-use discounts or enterprise terms.
How much should you budget for FASTQ, BAM, CRAM and VCF storage?
Start with the files you will retain, not just the input FASTQ. A typical budget worksheet should have separate rows for raw reads, aligned BAM or CRAM, index files, VCF and gVCF outputs, annotation databases, intermediate files, logs and duplicate or backup copies. Record size per sample, sample count, compression format and months retained.
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Active versus archive retention
Keep files that are queried or reprocessed frequently in active storage. Move infrequently accessed raw data or completed projects to archive only after checking retrieval fees, minimum retention and restore latency. Archive pricing can be dramatically lower, as illustrated by BioInsight’s 22.50 BIC/TB/month standard rate versus 2.00 BIC/TB/month archive rate, but a cheap archive is not free if you repeatedly restore the same dataset.
Intermediate files and retries
Intermediate alignment, sorting, duplicate-marking and recalibration files can briefly exceed the size of the final result. Failed tasks may leave temporary objects or trigger a second full attempt. Include a peak working-set allowance and a retry percentage in your estimate, then configure lifecycle rules to delete safe-to-remove intermediates.
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Count every planned export: delivery to a clinician, transfer to an institutional archive, replication to another region and analyst downloads. Keeping data in the cloud may be less expensive than repeatedly moving terabytes out, but compliance, backup and access requirements can override that choice.
A repeatable method to estimate your bill
- Define the workload. Identify whether you are running whole genomes, exomes, RNA-seq, panels or metagenomics, and record the number of samples and expected coverage.
- Name the workflow. Specify the language or application, reference build, aligner, caller, annotation steps and whether analysis is private, Ready2Run or a third-party app.
- Specify outputs and retention. List FASTQ, BAM/CRAM, VCF, gVCF, intermediate files and logs. Assign an active or archive period to each file class.
- Estimate resources. Record CPU, memory, accelerators if any, requested run-file-system capacity, runtime, concurrency and expected retries.
- Count operations. Include API requests, queries, ETL, de-identification, metadata indexing and any scheduled reprocessing.
- Measure data movement. Estimate uploads, cross-service transfers, cross-region copies and downloads in GiB or TiB.
- Apply price conditions last. After calculating usage, apply region, free tier, committed-use discount or enterprise-contract terms using the current vendor calculator or quote.
- Stress-test the estimate. Recalculate with more samples, a longer retention period, a failed-run rate and an additional export so the budget has an operational range rather than one optimistic number.
How to compare platforms fairly
| Comparison point | Questions to ask |
|---|---|
| Price predictability | Is usage priced per sample, per run, per resource-hour or in credits? Can a fixed workflow price change with data volume? |
| Compute and orchestration | Are CPU, memory, parallel tasks, retries and workflow-engine overhead metered separately? |
| Storage lifecycle | Are active and archive tiers available? Are there minimum retention, retrieval or restore charges? |
| Data movement | What do uploads, cross-region transfers and downloads cost, and where will the data be processed? |
| Operations and queries | Are API requests, ETL, de-identification, database queries or third-party apps billed independently? |
| Workflow support | Does the service support the language and tools your team uses, such as WDL, Nextflow or CWL? |
| Governance | Do the region, audit controls, identity model, retention policy and compliance terms meet your requirements? |
A platform with a higher per-run price may still be cheaper overall if it reduces engineering time and produces predictable sample costs. Conversely, a low storage rate can be overwhelmed by egress or repeated reprocessing. Compare a complete workflow scenario, not isolated price rows.
Common budgeting mistakes and fixes
Using a monthly subscription as the model
Most of the services described here meter usage or credits. Replace a guessed subscription with a workload-based sheet that shows compute, storage, operations and transfer separately.
Pricing only the final VCF
Raw reads, alignment files and intermediates often remain the largest retained objects. Include every file class and its retention tier.
Ignoring idle and temporary resources
Run file systems, unattached storage, staging buckets and failed-run outputs can continue generating charges. Add cleanup policies and inspect resource inventories after each project.
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Assuming a free allowance repeats
The AWS new-customer quantities apply to the first two months, and the BaseSpace 250-iCredit trial expires after 30 days. Model the post-trial workload at standard rates.
Comparing credits as if they were dollars
BaseSpace iCredits and BioInsight BIC are platform-specific units. Compare the credit requirement and the account’s purchase terms, not the numbers alone.
Forgetting regional and contractual terms
The Google Cloud figures cited are for Iowa and specified GiB ranges. AWS and other vendors can vary by region, discounts and enterprise agreement. Apply those conditions only after you have measured usage.
Which pricing approach fits your project?
Small, standardized sample batches
A fixed per-run workflow or credit schedule can be easiest to explain to a project manager. BaseSpace’s published iCredit examples provide a starting point for sample-oriented planning, provided storage and account limits are added.
Custom pipelines and variable workloads
Metered infrastructure such as HealthOmics private workflows or an API-based Google Cloud design gives more control over tools and scaling. It requires a resource model, lifecycle automation and monitoring to prevent surprises.
Long-term repositories
Prioritize archive tiers, retrieval policy and data-governance controls. The lowest storage rate is not automatically the lowest total cost if users must restore and download the same data repeatedly.
Bottom line for planning
Budget cloud genomics by sample and by month, but calculate the underlying resources that create those units. For each scenario, show compute, run space, active and archive storage, requests or application credits, data transfer and the retention period. Use the published AWS, Google Cloud and Illumina figures as anchors, then replace them with current regional prices or contract terms before committing funds.
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