Get your NGS analysis started in minutes with Basepair

Web-based: No software to install

Sign-up online in less than a minute, no software to install, manage and upgrade. No hardware required either. Your samples and results are available at your office, home or conference, 24-7.

Easy to use: Run analyses in minutes

Run complex workflows with just a few clicks. Most users take less than a minute of hands-on time to add a sample and run an analysis. Our workflows show all the steps of the analysis to help the users understand exactly how their data will be analyzed.

Reports: Understand your data with a quick glance

Every Basepair analysis provides a rich clutter-free report with important stats and figures. With a quick glance, understand your sample and analysis trends. Our reports are also useful for checking how well the experiment worked.

Comprehensive workflows: From QC to figures in one go

Basepair provides several high quality workflows for most NGS applications. We constantly evaluate the latest genomics tools and string together the best pipeline to provide a comprehensive analysis of your data. When no public software suffices, we develop our own module to generate the relevant results. Our workflows are fully automated; a single click generates all the results.

In addition to the public workflows, users may create custom private workflows. Our cloud architecture supports programs written in any language or environment.

DNA-Seq: QC, Alignment, Process reads, Variant calling, Annotation

RNA-Seq: QC, Alignment, Expression count, Differential expression

ChIP-Seq: QC, Alignment, Peak calling and annotation, Motifs

ATAC-Seq: QC, Alignment, Peak calling and annotation, open chromatin regions

Execute the biggest genomics projects


Fast: Get results in a few hours

Basepair’s unique technology ensures you get your results in a few hours, whether you have 10 samples or 10,000. Your analysis starts right away, there is never a wait time. We use servers with up to 32 cores, SSD disks and enhanced networking to ensure you get your results quickly. Many of our algorithms are optimized to run in parallel.

Scalability: Run 1000+ analysis in parallel

Basepair is ready to handle the workload of the largest genome projects. Our scale-out architecture fires up servers as users request a new analysis and automatically shuts them down upon completion of the analysis. We have the capacity to run 1000s of multi-core servers to support the biggest workloads.


Unlimited storage: Never delete a file again

Running on top of highly capable cloud providers, we offer our users virtually unlimited storage that is secure, encrypted and durable. We automatically store raw data, intermediate files and final results. Being web-based, your data is available across the globe with an Internet access.

Enterprise ready


Security: Your data is safe

We meet or exceed industry standards to keep your data safe from malicious agents. Both our web interface and API are https only, encrypting all information between your computer and our servers. All the data is encrypted at rest during storage. Our servers operate behind secure firewall.

Privacy: Control your data

We understand your data is highly valuable. You have complete control over who has access to your data; it is accessible to only you or other users on Basepair you have explicitly permitted to view/edit your data.


Audit: Stay on top

Any big project has multiple stakeholders; viewing, adding and editing data. Basepair diligently tracks all activities so you always know who did what and when. Every user activity is systematically stored and is available for review. In many cases, it is possible to roll back changes if required.

Support: For scientists, by scientists

We understand that a software is not going to answer all your questions. Basepair’s team of scientists are here to help you with both technical (how to use the software) and scientific (how to interpret your data) issues. We provide support over email, phone or in-person. We provide scientific consultation services for complex questions, e.g, data integration, making figures for publications, etc.

SLA: Because your project can’t wait

We probably dislike downtime more than you do. Our users trust us with important projects and we take our responsibilities very seriously. Basepair architecture is designed to be robust and fault-tolerant. We strive to provide an availability of 99.9%. Our systems were fully functioning for 99.8% in the last 12 months and 100% in the last 30 days.