For Pharma and Biotech R&D

Speed Up Your R&D Processes With Basepair’s Custom Pipelines

Save your research team weeks of work with custom pipelines

For many pharma and biotech companies, accelerating the pace of R&D is critical to staying competitive. One of the biggest bottlenecks in R&D is data analysis: building up an in-house bioinformatics team, setting up servers, and creating custom pipelines is both time-consuming and costly. With Basepair, it doesn’t have to be.

We set up and maintain the cloud infrastructure, build custom analysis pipelines, and provide bioinformatics support for your team. With such a robust analysis solution, your team can focus on what matters most, from assay development to drug discovery.


Enable seamless reproducibility you can’t get with internal tools

Audit trails are difficult to manage with manual NGS data analysis pipelines. Is your team keeping track of the tools it’s using? What about software versions, usage logs, and custom scripts?

With Basepair, you can focus on R&D without having to worry about tracking background processes. Basepair’s robust audit trails allow anyone to easily bring up logs months or years down the line. The platform automatically generates a log entry with each analysis, providing a traceback for what files and programs were used to generate the results.


Optimize your analysis process to speed up your R&D

Our cloud-native solution scales to thousands of parallel workflows and integrates seamlessly with LIMS and local databases. Advance innovation and save research teams weeks of work with cost-effective parallelization, a robust API, and built-in data trails for reproducible




How we helped EpiCypher build a custom  pipeline to accelerate assay development


Epicypher is a biotech company that develops cutting-edge technologies for epigenetic and chromatin biology. Their flagship product, SNAP-ChIP, is a next-generation spike-in control for ChIP-Seq assays.


While SNAP-ChIP offers a greatly needed control for one of the most widely used assays in the epigenetics space, the technology is centered on the use of DNA-barcoded recombinant nucleosomes for ChIP-seq assay quantification. This requires a specialized analysis.

Without an in-house bioinformatics team, Epicypher faced a data analysis bottleneck. So they turned to Basepair to build a “one-click” analysis solution to speed up their assay development.


First, Basepair worked closely with scientists at EpiCypher to create a custom analysis pipeline suitable for SNAP-ChIP data. The results were verified and approved by EpiCypher’s research team. The team could now use the pipeline internally for R&D efforts.

Basepair then made the custom pipeline available on its automated SaaS platform. Beyond internal R&D, Epicypher can now direct customers using SNAP-ChIP to run a pipeline tailored to the assay.


“The automated pipeline developed by Basepair has accelerated our R&D efforts. This ‘one-click’ solution was easy to implement and allows our team to rapidly analyze SNAP-ChIP-seq data. Further, bioinformatic experts from the Basepair team are readily available for troubleshooting, customization, and expert feedback. This has really helped increase the pace and quality of our efforts to identify best-in-class histone PTM antibodies.”

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Find out how we can put custom pipelines to work for your team.