TABLE OF CONTENTS As filed with the Securities and Exchange Commission on September 11, 2025. UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM S-1 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 Bionano Genomics, Inc. (Exact name of registrant as specified in its charter) (State or other jurisdiction of incorporation or organization) (Primary Standard Industrial Classification Code Number) Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, California 921 ...

Core Viewpoint - Bionano Genomics is focusing on routine users of its optical genome mapping (OGM) systems and VIA™ software to drive revenue and gross profit, achieving a gross margin above 50% in Q2 2025, indicating a successful strategy shift [2][4]. Financial Results - Total revenue for Q2 2025 was $6.7 million, a decrease of 13% from $7.8 million in Q2 2024, primarily due to the discontinuation of clinical services [4]. - Consumables and software revenues increased by 16% compared to the prior year [4]. - Instrument revenue decreased from $2.3 million in Q2 2024 to $1.4 million in Q2 2025, reflecting the company's strategy to focus on routine users rather than new instrument placements [4]. - Adjusted for instrument sales and discontinued clinical services, combined revenue for consumables, software, and remaining services increased by 11% [4]. - The company sold 7,233 nanochannel array flowcells in Q2 2025, a 17% increase from 6,165 flowcells sold in Q2 2024 [4]. - Gross margin was 52% in Q2 2025, up from 33% in Q2 2024 [4][18]. - Operating expenses were reduced by 42% to $11.3 million, with non-GAAP operating expenses down by 53% to $8.8 million [4]. Business Highlights - The installed base of OGM systems increased by 4% to 378 at the end of Q2 2025 [4]. - The company achieved a record of 119 peer-reviewed publications, showcasing the growing utilization of OGM [4]. - Bionano announced upgrades to its VIA and Solve™ software, enhancing genomic data analysis capabilities [4]. - The American Medical Association established a second Category I CPT code for OGM use in cytogenomic genome-wide analysis [4]. 2025 Outlook - The company anticipates Q3 2025 revenue in the range of $6.7 to $7.2 million and full-year 2025 revenue between $26.0 to $30.0 million [11]. - Expectations for new OGM installations have been increased to 20 to 25 for the full year 2025 [11]. - The company ended Q2 2025 with cash and equivalents totaling $27.4 million, providing a cash runway into the first quarter of 2026 [4][11].