Uploaded August 2026 | Updated September 2026, 2 weeks ago
Assembly-based DNA synthesis is emerging as a promising strategy to scale DNA data storage. However, this approach introduces structural constraints—such as fragment overlaps, motif restrictions, and length limits—that fundamentally reshape the encoding problem. These constraints influence not only how digital information is translated into DNA sequences, but also how fragments must be organized to support efficient molecular assembly and reliable data recovery.
In this work, we extend the proprietary end-to-end simulator DNAssim to support assembly-based synthesis workflows. The framework explicitly models assembly constraints during simulation and integrates assembly-aware encoding and validation procedures. In addition, we introduce novel clustering algorithms designed to organize DNA fragments while respecting assembly requirements. Clustering plays a central role in this process: fragments must be grouped in ways that preserve valid overlaps, avoid problematic sequence motifs, and maintain compatibility with downstream assembly protocols.
By capturing the interaction between encoding constraints, fragment organization, and assembly requirements, DNAssim enables systematic exploration of assembly-aware DNA storage designs. The framework allows researchers to evaluate how fragment structure, overlap strategies, and clustering approaches influence overall system performance. In particular, it provides a flexible platform to study how fragment organization impacts scalability, storage efficiency, and robustness during both synthesis and decoding.
Presented by
Alessia Marelli, Avaneidi
This is a presentation from the 2026 Storage and Computing with DNA Conference.
· Learn More about the SNIA DNA Data Storage Alliance: snia.org/groups/snia-dna-technology-affiliate
· SNIA Educational Library: snia.org/library
· X: twitter.com/SNIA
· LinkedIn: linkedin.com/company/snia
Assembly-based DNA synthesis is emerging as a promising strategy to scale DNA data storage. However, this approach introduces structural constraints—such as fragment overlaps, motif restrictions, and length limits—that fundamentally reshape the encoding problem. These constraints influence not only how digital information is translated into DNA sequences, but also how fragments must be organized to support efficient molecular assembly and reliable data recovery.
In this work, we extend the proprietary end-to-end simulator DNAssim to support assembly-based synthesis workflows. The framework explicitly models assembly constraints during simulation and integrates assembly-aware encoding and validation procedures. In addition, we introduce novel clustering algorithms designed to organize DNA fragments while respecting assembly requirements. Clustering plays a central role in this process: fragments must be grouped in ways that preserve valid overlaps, avoid problematic sequence motifs, and maintain compatibility with downstream assembly protocols.
By capturing the interaction between encoding constraints, fragment organization, and assembly requirements, DNAssim enables systematic exploration of assembly-aware DNA storage designs. The framework allows researchers to evaluate how fragment structure, overlap strategies, and clustering approaches influence overall system performance. In particular, it provides a flexible platform to study how fragment organization impacts scalability, storage efficiency, and robustness during both synthesis and decoding.
Presented by
Alessia Marelli, Avaneidi
This is a presentation from the 2026 Storage and Computing with DNA Conference.
· Learn More about the SNIA DNA Data Storage Alliance: snia.org/groups/snia-dna-technology-affiliate
· SNIA Educational Library: snia.org/library
· X: twitter.com/SNIA
· LinkedIn: linkedin.com/company/snia
