Scale Biosciences and Basepair to Democratize Single Cell Sequencing Data Analysis

SAN DIEGO — Scale Biosciences, a pioneer in single-cell sequencing technology, today announced a new collaboration with Basepair to provide point and click bioinformatic analysis of single-cell data produced with its patented and disruptive combinatorial indexing technology. As a result of this collaboration, scientists will be able to access Scale Biosciences’ optimized bioinformatics pipeline through a user-friendly, web-based, graphical user interface (GUI), enabling their organizations to quickly adopt new single-cell protocols, regardless of their in-house bioinformatics capabilities.

The initial deployment of the ScaleBio Seq Suite on the Basepair platform will allow researchers to upload both fastq and BCL files and use an intuitive GUI to quickly analyze their data and generate reports for individual samples and entire libraries. These include reports to help researchers assess their data quality and produce a cell-gene matrix compatible with open-source standard single-cell analysis workflows like Seurat and Scanpy. The collaboration will also make it easier for customers to adopt Scale Biosciences technology without investing in additional IT and bioinformatics infrastructure by providing a secure way to upload and store data in the cloud.

“Challenges related to analysis and interpretation of sequencing data are still one of the most common bottlenecks that researchers face when adopting new next-generation sequencing applications, especially those that create large amounts of data,” said Giovanna Prout, CEO of Scale Biosciences. “We want the scientific community to have access to bioinformatics options that fit their budget and help answer their research questions. Through our relationship with Basepair, we are making it easier for organizations with limited resources to quickly and cost effectively go from sample to interpretable data.”

“At its core, Basepair enables tools manufacturers like Scale Biosciences to better support research scientists with any computational background,” said Amit Sinha, PhD, Founder of Basepair. “With our groundbreaking federated approach to analysis, we look forward to helping Scale Biosciences’ customers better understand their data and accelerate their research without it ever needing to leave their direct control.”

Learn more about Scale Biosciences single-cell technology at

About Scale Biosciences

ScaleBio is a single-cell sequencing solutions company founded by a multidisciplinary team of scientists and technologists with combined expertise in next-generation sequencing, genomics, proteomics, and bioinformatics, and a common mission for unlocking the potential of single-cell analysis at scale by eliminating barriers to discovery. ScaleBio is financed by leading life sciences tools investors ARCH Venture Partners, BNG and Tao Capital. ScaleBio has R&D facilities in San Diego and Menlo Park, CA.

About Basepair

Basepair Inc is a bioinformatics company focused on unlocking the full potential of next generation sequencing (NGS) technology. By empowering more scientists to understand the meaning and value of genomic data while keeping it secure in-place, we help accelerate the scientific and diagnostic breakthroughs that bring lifesaving medicines and treatments to the patients that need them. To learn more, visit

CONTACT: Scale Biosciences

For Media – Gwen Gordon ([email protected])

For general inquiries – ([email protected])

Basepair Inc.

For media – Simon Valentine ([email protected])

For general inquiries – Sam Steffan ([email protected])

< | >