Comprehensive variant discovery.

You’ve sequenced whole genomes – why not find all forms of genetic variation? Base2 Genomics provides a scalable and comprehensive platform for characterizing all forms of genetic variation, including structural and copy number variation, short tandem repeat variation, aneuplodies and sex chromosome anomalies.

Highly scalable data processing.

The Base2 data processing platform is built upon Amazon Web Services and has been designed for economical scalability to many samples, even from whole genome sequencing. We have processed cohorts involving 1000s of human genome sequences in a matter of days.  Cohort data remain secure, siloed and processed on encrypted storage.

Structural variant visualization and quality contol

Base2 has developed several new technologies for visualizing and adjudicating structural variants. We provide interactive plots and reports of SVs meeting specific inheritance and phenotypic impact criteria.

Structural variant interpretation.

Base2 Genomics has developed STIX (STructural variant IndeX), a proprietary SV compression and database technology for efficiently profiling sequence alignment evidence for structural variation among thousands of human genomes. Much like gnomAD for SNP and INDEL variation, STIX facilitates SV interpretation in genomes you’ve sequenced by measuring their frequency large WGS cohorts such as 1000 Genomes, SFARI, Simons Genome Diversity Project, and more.

Extensive quality control

Quality control is critical to ensuring that no systematic artifacts, sample mix-ups, or unexpected data anomalies exist prior to commencing detailed analysis. Base2 Genomics provides extensive quality control tools, reports, and interactive visualizations that allow you to easily detail issues with sequencing coverage, unexpected ancestry or kinship, aneuploidy, or sex chromosome anomalies.

Base2 Technology Publications


A probabilistic framework for structural and copy number variant discovery (More)


A flexible framework for exploring variations within the human genome (More)

Genotype Query Tools

Instruments for the efficient analysis of large genetic-variation data sets (More)


Detecting and resolving sample anomalies in human DNA sequencing studies (More)


Algorithm for fast and flexible annotations of variations in genetics (More)