For Academic Researchers

Stop waiting and start publishing with Basepair’s online NGS analysis platform

Put yourself in the driver’s seat of your lab’s data analysis

Researchers often run into the same fundamental problems. You wait weeks for your bioinformatics core to analyze your NGS data. You wish, of course, that you could do the analysis yourself, but you’re not a bioinformatician. The good news? With Basepair, you can stop waiting and start analyzing data yourself. Basepair combines all the NGS analysis tools researchers need in a single, straightforward package that does not require any code and is easy to use.

Get beautiful visuals for publication in every analysis report

Do you ever wait weeks for analysis results only to get the output in long bleary files? At Basepair, we understand how crucial reporting and visuals are to downstream analysis – and what a pain it can be to set up. That’s why we include a host of visual and interactive components as part of the analysis report. You can even download high-resolution figures in png or vector format and add them to your posters or papers in just a few clicks.

Enjoy the credibility of open-source tools without the hassle of running them

Analyzing NGS data often involves a disjointed approach using various open-source tools that require multiple pieces of command line software, file conversion between programs, and wasted time waiting for various algorithms to finish. At Basepair, we’ve automated this process and combined multiple tools and steps into one-click pipelines. At the same time, all our pipelines are built on highly cited open-source tools so you can be confident in your results.



How MSKCC analyzed 200 NGS samples on Basepair, without a line of code.


Dr. Omar Abdel-Wahab’s lab at Memorial Sloan Kettering Cancer Center was studying the molecular mechanisms of ASXL2 – a frequently mutated gene in acute myeloid leukemia patients with the AML1-ETO fusion oncoprotein.


The lab had 200 NGS samples that had already been sequenced and needed to be analyzed. However, none of the lab members were bioinformaticians, so the lab would have to find an external solution to get their samples analyzed. As is frequently the case, the university bioinformatics core was backlogged. Dr. Abdel-Wahab’s team needed an affordable NGS data analysis solution that would scale to a large number of samples and would be simple enough to use without needing to hire additional help.


Dr. Abdel-Wahab’s lab used Basepair to analyze their NGS data in just a few hours.  Even though the team had never analyzed NGS data before, Basepair’s simple, intuitive interface allowed the team to run 200+ analyses at scale on their samples.


“We first analyzed a few old datasets and Basepair results were as good or better than previous manual analysis. What we liked about Basepair was that they used the best available tools in the analysis pipeline, so the results were high quality and readily acceptable for publication. Basepair even let us deposit the data to the Gene Expression Omnibus with a few clicks.”

The data from the project was used to publish a paper in Nature Communications: ASXL2 is essential for haematopoiesis and acts as a haploinsufficient tumour suppressor in leukemia.

Full article.

Find out how we can help your lab start analyzing NGS data quickly.