Analyze your NGS data in hours

Upload your raw data, choose among several high quality workflows for RNA-Seq, ChIP-Seq, DNA-Seq, etc. and get results in an hour.
Start free trialLearn more

Trusted by scientists at

Our customers are saying

Fast, excellent and reasonably priced…you CAN get all three!! Thank you to the folks at Basepair for helping us deal with some difficult RNA Seq data.

Sharen Mckay

Yale University

I really like how easy the website is to use. And how quickly the results are generated, including figures. I would have never thought about doing a new analysis like I just did.

Emilie Montenont

NYU Langone Health

Support answers come fast and are always precise!

Maria Hollnagel

Ulm University

Features at a glance


Ready 24/7, signup and use online. No software to install, no hardware to buy.

Easy to Use

Run workflows with a few clicks, less than a minute hands-on time per sample.



Most workflows finish in an hour, multiple analyses in parallel, no wait time.

Workflows to go

Fully automated workflows for DNA-Seq, RNA-Seq, ChIP-Seq, ATAC-Seq, etc.


Basepair’s scientists are available to help over phone, email, or in-person.

Custom workflows

Develop and run custom workflows using any combination of public and private tools.


Use REST, Python API or CLI to automate and integrate large projects.



All data is encrypted during rest and transfer and servers behind firewall.

Analyze your NGS data today, get results in hours