OmicsBox includes a comprehensive set of algorithms and tools across its modules for genome, transcriptome, metagenome, genetic variation, and functional analysis workflows. While most tools are included within the subscription plan, certain resource-intensive processes such as alignments and assemblies consume Cloud Units when executed.
This article explains what Cloud Units are and provides guidance on how they are consumed by each algorithm. However, it is important to note that usage depends on factors such as input data size and selected algorithm parameters. Consumption can be monitored through the Cloud Usage section in OmicsBox, where each job reports runtime, input and output size, units consumed, and billed usage.
What are Cloud Units?
Cloud Units are a usage-based measure of computational resources consumed when running specific high-performance analyses in OmicsBox. They represent the underlying cloud infrastructure required to process data-intensive tasks, allowing users to access scalable computing power without the need for local hardware. One Cloud Unit corresponds to one CPU-second of compute time. For example, if an algorithm runs for one hour on eight CPUs, this results in 28,800 Cloud Units being consumed. As a result, both runtime and level of parallelization influence consumption.
Which features consume Cloud Units?
Here the list of tools which consume units as of OmicsBox Version 4. All other features are included without consuming units.
- Alignments: BWA, Bowtie 2, STAR, BWA
- Assembly: ABySS, SPAdes, Flye, Trinity, MEGAHIT, metaSPAdes
- Sequence Analysis: Diamond, NCBI Cloud and Custom Blast, InterProScan
Average Unit Consumption per Tool
The following table list the average consumptions of charged algorithms based on the average values from the history of completed jobs in OmicsBox.
| Feature Name | Type | Average Cloud Units Consumption | Total Runs / Cloud Units Package* |
|---|---|---|---|
| ABySS | Genome assembly | ~30,000 | ~200 |
| Bowtie 2 | DNA alignment | ~40,000 | ~150 |
| BWA | DNA / RNA alignment | ~40,000 (varies) | ~150† |
| MEGAHIT | Metagenome assembly | ~40,000 (varies) | ~150 |
| InterProScan | Domain scan | ~40,000–70,000 | ~85–150 |
| Diamond Blast | Similarity search | ~30,000–90,000 | ~70–200 |
| SPAdes | Assembly | ~70,000 | ~85 |
| NCBI Cloud Blast | Similarity search | ~100,000 (high variability) | ~60† |
| STAR | RNA-seq alignment | ~100,000 | ~60 |
| Trinity | RNA-seq de novo assembly | ~60,000–200,000 | ~30–100 |
| Flye | Long-read assembly | ~15,000 to ~200,000 (high variability) | wide range† |
| MetaSPAdes | Metagenome co-assembly | ~300,000 | ~20 |
*One package contain at the moment of writing 6,000,000 units and the amount of possible executions is an estimate based on average values.
Recommendations
If you have a normal research workload (regular alignments and assemblies, not a sequencing core that runs assemblies all day), the Cloud Units that come with a single-seat annual plan are often enough for the year. Only the tools listed earlier use billed units; most of OmicsBox does not touch that balance in the same way.
If you worry that one dataset could use a lot of Cloud Units, run one sample first. When that job is done, check Cloud Usage for it, then decide whether to launch the full set of samples. That way you avoid surprises.
To verify your usage, open View > Cloud Usage in OmicsBox (Desktop or Web) and review each job: how long it ran, how large the inputs and outputs were, how many Cloud Units it used, and whether those units counted against your balance. If your past jobs look like the numbers in the table, you get a feel for how units get consumed. If your jobs are much bigger or much smaller, your own Cloud Usage history is the best reference.
In any case, if your Cloud Unit balance drops below one million, BioBam will send you an email with guidance on how to recharge your account or set up an auto-recharge option.
If you still have doubts about your usage and Cloud Unit requirements, contact support@biobam.com so our support team can review your use case and match numbers.
About OmicsBox
OmicsBox is BioBam’s bioinformatics software for the analysis of omics data. It provides workflows for genome, transcriptome, and metagenome datasets, organised in five modules: Genome analysis, Transcriptomics, Genetic Variation, Functional analysis, and Metagenomics.
The Functional analysis module is based on the Blast2GO annotation methodology, with more than 10,000 citations in the scientific literature, and is widely used in non-model organism research.
Computationally demanding steps run in the cloud through OmicsCloud. OmicsBox itself runs on a standard PC or laptop under Windows, Linux, or macOS. Licensing is subscription-based, with flexible options.
Feedback, questions, and feature requests are welcome at support@biobam.com or through the BioBam account. Further information is available at biobam.com/omicsbox and in the user manual. Trade names: BioBam, OmicsBox, and Blast2GO as used by BioBam.
References
- BioBam. Cloud Computation (overview, pricing context, charged tool list). https://www.biobam.com/cloud-computation/
- BioBam. OmicsBox User Manual: Cloud Computation and Storage (Cloud Units, Cloud Sync, Cloud Files, Cloud Usage). https://docs.omicsbox.biobam.com/latest/Cloud-Computation-and-Storage/
About the Author
Dr. Stefan GötzStefan is the founder and CEO of BioBam. Since founding the company in 2011, he has focused on helping researchers simplify genomics and omics data analysis through practical and accessible software solutions. Under his leadership, BioBam has supported scientists and institutions worldwide in advancing research in human health, agriculture, and environmental science. Stefan remains closely involved in product strategy, innovation, and customer-driven development. He holds a Ph.D. in bioinformatics and combines scientific expertise with entrepreneurial leadership to make advanced bioinformatics more accessible to the global research community.
