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DOE OSTI2019

Tradeoffs in Prameter Values for Optional Performance

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2019

Final Report for Transmission of Information by Acoustic Communication along Metal Pathways in Nuclear Facilities

Transmission of information using elastic waves on existing metallic pipes provides an alternative communication option for a nuclear facility. The advantages of this approach consist of transmitting information through barriers, such as the containment building wall. A viable candidate for acoustic communication channel is a chemical volume control system (CVCS) stainless steel pipe, which penetrates through the containment building wall. A laboratory bench-scale system consisting of a nuclear grade CVCS-like pipe and ultrasonic transducers was assembled for a preliminary communication system analysis. Because of low bandwidth and spectral dispersion of ultrasonic transducers, on off keying (OOK) protocol was chosen for data communication. Operation of the acoustic communication during normal and post-accident conditions involves data transmission on the CVCS pipe, which according to literature guidelines, will be at 50°C and 150°C, respectively. Preliminary communication system development was performed using paintbrush PZT transducers capable of continuous operation at temperatures up to 80°C. Next, high-temperature LiNbO 3 acoustic transducers, originally developed for flow metering applications of EBRII reactor at Argonne, were utilized to develop a high-temperature acoustic communication system. A Gaussian pulse shape filter was introduced to suppress ringing and thus reduce inter-symbol interference. This resulted in enhancement of data transmission bitrate. Heating tapes, temperature controllers, and thermal insulation were installed on the laboratory pipe to study acoustic communication at elevated temperature. This included development of custom insertion heating elements for controlling temperature at pipe ends. Demonstrations of communication at high temperature included transmission of images and text files. Main achievements thus far include demonstration of transmission of 90KB image at the bitrate of 10Kbps with bit error rate smaller than 10 -3 across the pipe heated to 50°C and 150°C. Final phase of project development involved investigating strategies for deployment of the ultrasonic communication system in a representative environment. Mechanisms Engineering Test Loop (METL) facility at ANL was chosen as a viable candidate for communication system demonstration. Analysis of piping manifolds at METL has shown that in a typical scenario, ultrasonic signals have to be transmitted over straight and bent piping sections. This report describes preliminary studies on transmission of information with ultrasonic shear waves across bent piping sections. A test article consisting of a stainless steel pipe bent at 90° was developed for laboratory analysis of ultrasonic signal transmission. The bent piping test article developed by welding two straight pipes to an elbow. For consistency, the diameter and wall thickness of the bent pipe is the same as that of the straight pipe utilized in prior studies. COMSOL computer simulations were performed to study ultrasonic refracted shear wave coupling and transmission across bent piping. Preliminary evaluations of ultrasonic shear wave transmission were conducted with piezoelectric (PZT) and LiNbO 3 transducers, with the signals recorded with previously developed LabView interface. Preliminary results have shown significant dispersion of transmitted signals, most likely due to reflections and scattering by piping welds. Signal distortion compensation algorithm based on time reversal modulation (TRM) was initially investigated for transmission through solids, and demonstrated for signals transmitted over the bent pipe. Using TRM, it was shown that communication bitrates of 100Kbps were achievable, in principle.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2017

Basic Energy Sciences Roundtable: Opportunities for Quantum Computing in Chemical and Materials Sciences

Fundamental transformations in the basic logic of computing are few and far between. Since the invention of digital computers in the early 1940s, the logic underlying computation has remained the same, even as computing hardware evolved from vacuum tubes to silicon transistors. With the advent of quantum computation, a fundamental transformation is near. Quantum computation is based on a different type of logic: rather than being in one of the two states of a classical bit, a quantum bit or qubit can be in a superposition of two states simultaneously. Operations and measurements on these qubits obey the constraints of quantum mechanics. It is now understood that quantum computers have great power in principle to go beyond classical computers, but that not every application is well suited to implementation on quantum computers. For reasons explained in more detail in the Introduction, scientific problems in chemical and materials sciences are uniquely suited to take advantage of quantum computing in the relatively near future. Indeed, quantum computing offers the best hope to solve many of the most important and difficult problems in this field. For example, quantum materials, such as superconductors and complex magnetic materials, show novel kinds of ordered phases that are natural from the point of view of quantum mechanics but difficult to access via computation on classical computers. Quantum sensors based on solid materials are already widely used but could be greatly improved with insight from quantum computations, as could materials for information technologies. Quantum chemical dynamics is another example of a problem that is intrinsically well suited to studies on quantum computers. Applications of quantum chemical dynamics include catalysis, artificial photosynthesis, and other industrially important processes. Quantum computers exist in the laboratory and are beginning to exceed 50 qubits, which is roughly the size beyond which their behavior cannot be predicted or emulated on present-day classical supercomputers. While a quantum computer of 50 qubits is almost certainly not powerful enough to tackle the major scientific challenges in chemical and materials sciences, some of these major challenges start to become accessible with a few hundred qubits if error rates can be kept small. This roundtable was convened to ask how emerging quantum computers can be applied to major scientific problems in chemical and materials sciences, in light of Basic Energy Sciences’s leading role in these fields and the Department of Energy’s leading role in high-performance scientific computation more generally. The main outcome of the roundtable was a consensus that there are scientific problems of great importance on which emerging quantum computers have the potential for disruptive impact, and where comparable progress is unlikely to occur by other means.

36 MATERIALS SCIENCE↗

DOE OSTI2024

HPE ultralit project (ARPA-E open program 2018) final report 15

The goal of the program was to build a fully integrated optical transceiver with >1 Tb/s and <1.5 pJ/bit operating at 50 ◦ C. Optical transceivers are critical components in high-performance-computers (HPC) and data centers, and the details of their implementation has a big impact on the total power consumption (energy efficiency) of an HPC system. Our proposed transceiver used three key enabling technologies. Firstly, SiGe avalanche photodetectors have record-low sensitivities, meaning that they can reach low bit error rates with very little light input. As a result, we can drive our lasers at a lower drive current, thus saving electrical power. Secondly, we use MOS-based capacitive tuning in our deinterleaver, modulator, and demultiplexer. Capacitive tuning allows for the tuning of photonic elements with zero static power consumption. Thirdly, we use quantum dots as the gain material in our light source. This allows us to efficiently use our light source at temperatures that are typically encountered in an HPCsystem. Our proposed optical transceiver consisted of a quantum dot comb laser as a light source, a booster SOA, MOS-based deinterleavers, MOS based ring modulators, MOS-based ring demultiplexers, and SiGe APDs.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

LEED: A Lightwave Energy-Efficient Datacenter

The Lightwave Energy-Efficient Datacenter (LEED) program is a disruptive “green-field” approach that provides a quantum leap in the energy efficiency of datacenters. LEED’s fundamental value proposition is that a novel and re-architected optical network—RotorNet— can deliver “more bandwidth per buck” as well as unique system-level attributes that significantly improve overall datacenter energy efficiency and performance. LEED has developed three system-level testbeds. The first testbed uses calibrated hardware and software power measurements to determine server energy efficiency as a function of network bandwidth and workload. These measurements have shown that increasing network communications bandwidth dramatically increases server energy efficiency providing a realistic path to the overall ENLITENED program goal of doubling the number of transactions per joule. The second testbed demonstrates key hardware: a prototype low-loss, high-port count optical “selector switch”. This switch was fabricated, racked, and tested. Measured switch characteristics include loss, bandwidth, crosstalk, switch time, system-level switch time (including the transceivers), and bit error rate. The third testbed demonstrates a fully working and manufactured pinwheel design which dramatically lowers the cost of design, while delivering high switch radix and low reconfiguration times. The LEED project has tied these three novel photonic switch prototypes together with production servers and software through the development of a novel FPGA-based NIC platform called Corundum. Corundum ensures that the packet-switched protocols supported by commodity operating systems and devices can interface with the Rotor switch design. The LEED group has used this combined hardware and software prototype to characterize applications running at a commercially relevant scale. The project has used a combination of enhanced optical modulation amplitude (OMA) modulators, broadband multiplexers and demultiplexers, avalanche photodiodes, and a novel burst-mode receivers to enable the insertion of LEED-developed optical switches without the need for expensive optical amplification. Our modeling has shown that measured LEED-developed device characteristics can achieve link characteristics of 2 pJ/bit including both transceivers and the Rotor switch. In summary, the LEED program has demonstrated a credible and practical path, through novel hardware and software, to realize the program objectives of ENLITENED. The net result will ensure that the United States maintains its strength in the crucial sector of Information Technology, which is vital to both our economic security and our national security.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Integrated Spatial, Spectral, & Temporal Optical Reflectance System for Precision Occupancy & Location Sensing to Improve Building Energy Efficiency

Buildings consume approximately 35% of the electricity used in the U.S. and building owners can significantly reduce this energy use by providing services like heating, electrical power and lighting only when people are present. The ARPAe funded program titled “INTEGRATED SPATIAL, SPECTRAL, & TEMPORAL OPTICAL REFLECTANCE SYSTEM FOR PRECISION OCCUPANCY & LOCATION SENSING TO IMPROVE BUILDING ENERGY EFFICIENCY” demonstrates how a low cost sensor technology developed for measuring distances can be used to count and locate occupants with a high degree of precision with a very low error rates. This platform tells a building control system where occupants are located (but not who they are) so that energy consuming services can be provided only when the services are needed by building occupants. The original proof of concept involved using low cost, commercially available time-of-flight (TOF) sensors that measure distance, but the performance of these existing sensors was lacking, as they could not operate properly in the presence of sunlight, which blinded the simple TOF sensors and limited their utility in buildings. This project proposed a powerful new class of TOF sensors that used state-of-the-art integrated circuit (IC) fabrication processes that combined advanced photonics with conventional silicon chip circuitry for improved sensor performance. An equally important part of this project was to find ways to maximize occupant count and location accuracy while using the fewest number of sensors possible, in order to keep costs low. By using building blueprints to create digital twins of commercial building spaces, the team developed new algorithms to maximize occupant count and tracking accuracy by properly locating the minimum number of sensors at just the right spots in the building. This capability not only minimizes system costs but also simplified sensor installation and system commissioning. Our simulations of our sensor networks for a range of commercial floorplan designs demonstrated that our installed cost target of $0.08/sqft was attainable, though not fully demonstrated during the project. Finally, we noted that the TOF sensor concept could provide a valuable role in health and eldercare by tracking patients without the need for worn sensors and would be useful for fall detection and other patient safety metrics, including tracking healthcare/patient interactions. We feel that, when fully developed, this new class of sophisticated TOF sensors and support software will be a powerful new approach to improving building energy efficiency based on occupant centric control platforms and will also open new levels of patient safety in healthcare operations. To realize this potential, the team formed the Troy Sensor Company LLC to oversee licensing of the programs patents and continue to seek commercialization of this program’s activity sensing technologies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Hybrid Quantum Networks with Discrete Polarizations and Continuous Quadrature Variables

Final Scientific/Technical Report for DOE Project DE-SC0022069. Quantum communication and computation systems have evolved along two largely independent paradigms: discrete-variable (DV) systems that encode information in qubits such as photon polarizations or photon-number states, and continuous-variable (CV) systems that encode information in optical field quadratures. Each approach offers distinct advantages—DVs provide low error rates and compatibility with single-photon platforms, while CVs support deterministic operations and efficient quantum state manipulation. A fundamental challenge for building a scalable Quantum Internet lies in interfacing these two regimes into a unified hybrid architecture that can coherently distribute and process quantum information across heterogeneous quantum nodes. This project aims to develop and demonstrate a hybrid optical quantum network that seamlessly integrates DV and CV systems. Specifically, we investigate a new class of hybrid entanglement between the discrete polarizations of single photons and the continuous quadrature variables of optical cat states, overcoming incompatibilities in existing DV–CV demonstrations. Using this new entanglement resource, the team investigates a multi-node hybrid quantum local area network (Q-LAN) testbed capable of DV–CV entanglement generation, swapping, and distribution across fiber links.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

LDRD FY25 Program Overview

As Lawrence Livermore National Laboratory’s (LLNL’s) Laboratory Directed Research and Development (LDRD) program enters its fifth decade of leading-edge research and development, its impact and importance have never been stronger. The program continues to advance strategic investments in pioneering science, technology, and engineering, ensuring LLNL will be ready to deliver on our mission as it evolves over the coming decades. Investing in LDRD research, and the people who perform this critical work, gives LLNL the ability to sustain our role as a leader in the Department of Energy and National Nuclear Security Administration enterprise. The LDRD program enables high-risk, high-payoff research that anticipates emerging threats and future mission needs. By nurturing the ingenuity of the Lab’s greatest asset, its people, LDRD funding advances not only our research but also grows and nurtures our workforce: engaging future innovators with student mentoring, challenging postdoctoral researchers to apply their skills to support national security, and strengthening the leadership skills of early career staff. This annual report documents how LDRD investments advance LLNL’s science, technology, and engineering across our mission space. To assess LDRD’s impact we track both short and long-term metrics such as peer-reviewed publications, number of students, or professional fellows. In addition to reviewing these metrics, I encourage you to delve deeper into the breadth of science and technology that illustrate the strategic value of this research portfolio. For instance, a recent exploratory research project used advanced manufacturing to construct miniaturized three-dimensional ion traps for a quantum computer with reduced quantum error rates to enable applications that address national security missions and support basic science. Another project has delved into studying detonation by examining deflagration to enhance the safety and security of the nuclear weapons stockpile. LDRD researchers are also deploying AI agents on two of the world’s most powerful supercomputers to automate and accelerate inertial confinement fusion experiments. Other teams are delivering more accurate optical constants to enable improved validation for aluminum to advance atomic and molecular physics models. LDRD-driven discoveries of how metals deform under extreme conditions strengthen our ability to model and design materials for demanding national security environments. National security challenges are increasingly complex and continuously evolving. LDRD focuses our most innovative science and technology on these challenges, ensuring the Laboratory is developing creative, forward-leaning solutions for our nation and the world. The following pages feature highlights of published scientific advances, patents, and honors that stem from LDRD investments. As you read this report, I hope you will understand how these investments position the Laboratory, and our partners, to meet the demands of the decades ahead.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity

Background: The advent of the Single-Molecule Real-time (SMRT) Isoform Sequencing(Iso-Seq) has paved the way to obtain longer full-length transcripts. This method was found tobe much superior in identifying full-length splice variants and other post-transcriptional events ascompared to the Next Generation Sequencing (NGS)-based short read sequencing (RNA-Seq).Several different bioinformatics tools to analyze the Iso-Seq data have been developed and someof them are still being refined to address different aspects of transcriptome complexity. However, acomprehensive summary of the available tools and their utility is still lacking. Objective: Here, we summarized the existing Iso-Seq analysis tools and presented an integratedbioinformatics pipeline for Iso-Seq analysis, which overcomes the limitations of NGS and generateslong contiguous Full-Length Non-Chimeric (FLNC) reads for the analysis of posttranscriptionalevents. Results: In this review, we summarized recent applications of Iso-Seq in plants, which include improvedgenome annotations, identification of novel genes and lncRNAs, identification of fulllengthsplice isoforms, detection of novel Alternative Splicing (AS) and Alternative Polyadenylation(APA) events. In addition, we also discussed the bioinformatics pipeline for comprehensiveIso-Seq data analysis, including how to reduce the error rate in the reads and how to identify andquantify post-transcriptional events. Furthermore, the visualization approach of Iso-Seq was discussedas well. Finally, we discussed methods to combine Iso-Seq data with RNA-Seq for transcriptomequantification. Conclusion: Overall, this review demonstrates that the Iso-Seq is pivotal for analyzing transcriptomecomplexity and this new method offers unprecedented opportunities to comprehensively understandtranscripts diversity.

Biochemistry & Molecular Biology↗

DOE OSTI2022

A Logarithmic Bayesian Approach to Quantum Error Detection

We consider the problem of continuous quantum error correction from a Bayesian perspective, proposing a pair of digital filters using logarithmic probabilities that are able to achieve near-optimal performance on a three-qubit bit-flip code, while still being reasonable to implement on low-latency hardware. These practical filters are approximations of an optimal filter that we derive explicitly for finite time steps, in contrast with previous work that has relied on stochastic differential equations such as the Wonham filter. By utilizing logarithmic probabilities, we are able to eliminate the need for explicit normalization and can reduce the Gaussian noise distribution to a simple quadratic expression. The state transitions induced by the bit-flip errors are modeled using a Markov chain, which for log-probabilities must be evaluated using a LogSumExp function. We develop the two versions of our filter by constraining this LogSumExp to have either one or two inputs, which favors either simplicity or accuracy, respectively. Using simulated data, we demonstrate that the single-term and two-term filters are able to significantly outperform both a double threshold scheme and a linearized version of the Wonham filter in tests of error detection under a wide variety of error rates and time steps.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Superconducting Radio Frequency Resonators for Quantum Computing: A Short Review

Superconducting radiofrequency (SRF) technology is being used not only in discovery science programs and basic research but also for several applications that benefit society more directly. The advantage of superconducting resonators over those made of normal-conducting metal is their ability to store electromagnetic energy with much lower dissipation. The high-quality factor and longer dissipation time provided by these superconducting resonators can deliver superior performance. Currently, the quantum processing architecture uses resonators and interconnecting circuits operating in the microwave regime with superconducting strip-line technology and low noise electronic devices for switching and communication. The performance of these devices can be enhanced by embedding them in 3D SRF cavity resonators to prolong the coherence time, which improves the utility of the device by reducing error rates and allowing more manipulations (calculations) before the quantum state decays. Here, we present a short review of current microwave technology used in quantum computers and progress towards the 3D resonators to enhance thecoherence time.

Dhakal, Pashupati↗

DOE OSTI2022

Characterizing the Reproducibility of Noisy Quantum Circuits

The ability of a quantum computer to reproduce or replicate the results of a quantum circuit is a key concern for verifying and validating applications of quantum computing. Statistical variations in circuit outcomes that arise from ill-characterized fluctuations in device noise may lead to computational errors and irreproducible results. While device characterization offers a direct assessment of noise, an outstanding concern is how such metrics bound the reproducibility of a given quantum circuit. Here, we first directly assess the reproducibility of a noisy quantum circuit, in terms of the Hellinger distance between the computational results, and then we show that device characterization offers an analytic bound on the observed variability. We validate the method using an ensemble of single qubit test circuits, executed on a superconducting transmon processor with well-characterized readout and gate error rates. The resulting description for circuit reproducibility, in terms of a composite device parameter, is confirmed to define an upper bound on the observed Hellinger distance, across the variable test circuits. This predictive correlation between circuit outcomes and device characterization offers an efficient method for assessing the reproducibility of noisy quantum circuits.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Accuracy, Bias, and Improvements in Mapping Crops and Cropland across the United States Using the USDA Cropland Data Layer

The U.S. Department of Agriculture’s (USDA) Cropland Data Layer (CDL) is a 30 m resolution crop-specific land cover map produced annually to assess crops and cropland area across the conterminous United States. Despite its prominent use and value for monitoring agricultural land use/land cover (LULC), there remains substantial uncertainty surrounding the CDLs’ performance, particularly in applications measuring LULC at national scales, within aggregated classes, or changes across years. To fill this gap, we used state- and land cover class-specific accuracy statistics from the USDA from 2008 to 2016 to comprehensively characterize the performance of the CDL across space and time. We estimated nationwide area-weighted accuracies for the CDL for specific crops as well as for the aggregated classes of cropland and non-cropland. We also derived and reported new metrics of superclass accuracy and within-domain error rates, which help to quantify and differentiate the efficacy of mapping aggregated land use classes (e.g., cropland) among constituent subclasses (i.e., specific crops). We show that aggregate classes embody drastically higher accuracies, such that the CDL correctly identifies cropland from the user’s perspective 97% of the time or greater for all years since nationwide coverage began in 2008. We also quantified the mapping biases of specific crops throughout time and used these data to generate independent bias-adjusted crop area estimates, which may complement other USDA survey- and census-based crop statistics. Our overall findings demonstrate that the CDLs provide highly accurate annual measures of crops and cropland areas, and when used appropriately, are an indispensable tool for monitoring changes to agricultural landscapes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

A Cascaded Random Access Quantum Memory

Dynamic random access memory is critical to classical computing but notably absent in experimental quantum computers. Here we realize an 8-bit cascaded random access quantum memory using superconducting circuits and cavities and showcase the ability to perform arbitrary gate operations on it. In addition to individual error channels such as photon loss, quantum memories can also experience decoherence from many-body self-interaction. We characterize the origin and contributions of many-body infidelity throughout the memory cycle. We find that individual modes can be accessed with $\lesssim 1.5\%$ infidelity per mode and that the entire memory can be accessed in arbitrary order with an error rate below the depolarization threshold of the surface code, paving the way for fault-tolerant quantum memories.

Li, Ziqian [Stanford U., Appl. Phys. Dept.; Stanfo↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2019

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1966

Gemini orbital tracking.

Simulation testing pilot performance in orbiting Gemini spacecraft based on tracking rate errors and fuel consumption

ASTRONAUT PERFORMANCE↗