Using synthetic DNA for data storage and for physical information encoding in labeling, tracing, and authentication applications is becoming more feasible as synthesis and reading technologies are improving. DNA in data storage applications has several advantages such as very high physical density and robustness. Some of the new synthesis technologies lead to repetition noise, consisting of sticky insertions and deletions in the resulting messages. In this paper, we address reconstruction algorithms for multiple trace communication channels with repetition (sticky insertion and deletion) noise. We prove correctness and analyze failure rates, both analytically and on simulated data. We identify a failure mechanism related to alternating stretches in the design sequence that leads to a potential bias in the data derived from reads (traces) and used for reconstruction. To minimize this effect we introduce alternating length limited codes (ALL codes) and analyze some of their properties.

Synthetic DNA is an attractive alternative for data storage media due to its high information density, low energy usage, and exceptional robustness. Enzymatic DNA synthesis was recently introduced to allow cost effective synthesis of longer DNA molecules for data storage. This method is characterized by stutter errors which are sticky insertions so that every base in the designed sequence may be synthesized more than once. In this work, we study the problem of reconstructing the original sequence from a set of noisy reads originating from the stuttering enzymatic synthesis. We present different reconstruction algorithms and analyze their expected success probability and error rate for three different scenarios that depend on the information which is known about the stutter errors. We evaluate algorithmic performance analytically as well as by using simulations. We are especially interested in characterizing the performance as a function of the read depth. Our findings can be used to evaluate the trade-offs between synthesis quality indicators and the sequencing depth required for reconstruction with high probability. In principle, the probability of reconstruction failure exponentially decays with the sequencing depth, as demonstrated in the study. We also analyze the use of error-correcting codes to improve the error performance.

MOTIVATION: Recent years have seen a growing number and an expanding scope of studies using synthetic oligo libraries for a range of applications in synthetic biology. As experiments are growing by numbers and complexity, analysis tools can facilitate quality control and support better assessment and inference. RESULTS: We present a novel analysis tool, called SOLQC, which enables fast and comprehensive analysis of synthetic oligo libraries, based on NGS analysis performed by the user. SOLQC provides statistical information such as the distribution of variant representation, different error rates and their dependence on sequence or library properties. SOLQC produces graphical reports from the analysis, in a flexible format. We demonstrate SOLQC by analyzing literature libraries. We also discuss the potential benefits and relevance of the different components of the analysis. AVAILABILITY AND IMPLEMENTATION: SOLQC is a free software for non-commercial use, available at https://app.gitbook.com/@yoav-orlev/s/solqc/. For commercial use please contact the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The consumer drone market has shown a constant growth for the past few years. As drones become increasingly autonomous and used for a growing number of applications, it is crucial to establish parameters for collocated human-drone interaction. Prior research showed how ground robots should approach a person to initiate interaction. This paper builds upon prior work and investigates how a flying robot should approach a person. Because of the flight capability, drones present more approach parameters than ground robots and require further study to properly design future interactions. Since research methodologies in aerial robotics are not well established, we present a taxonomy of methodologies for human-drone interaction studies to guide future researchers in the field. This paper then contributes a user study (N=24) investigating proximity, speed, direction, and trajectory towards a comfortable drone approach. We present our study results and design guidelines for the safe approach of a drone in a collocated indoor environment.