iGenomics: Comprehensive DNA sequence analysis on your Smartphone

OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier

Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in both clinical and environmental health, e.g., detection of bacterial outbreaks. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. For instance, metagenomics classifiers usually require a large amount of memory or specific operating systems/libraries. In this work, we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases (e.g., selection of bacteria of public health priority), making it ideal for running on smartphones or tablets. We indexed both OCTOPUS and Kraken2 on a bacterial database with ~4,000 reference genomes, then simulated a positive (bacterial genomes from the same species, but different genomes) and two negative (viral, mammalian) Nanopore test sets. On the bacterial test set OCTOPUS yielded sensitivity and precision comparable to Kraken2 (94.4% and 99.8% versus 94.5% and 99.1%, respectively). On non-bacterial sequences (mammals and viral), OCTOPUS dramatically decreased (4- to 16-fold) the false positive rate when compared to Kraken2 (2.1% and 0.7% versus 8.2% and 11.2%, respectively). We also developed customized databases including viruses, and the World Health Organization's set of bacteria of concern for drug resistance, tested with real Nanopore data on an Android smartphone. OCTOPUS is publicly available at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.

Beyond assembly: the increasing flexibility of single-molecule sequencing technology

The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.

Real-time genomics for One Health

The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.

Portable nanopore-sequencing technology: Trends in development and applications

Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.

KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing

Nanopore technology enables portable, real-time sequencing of microbial populations from clinical and ecological samples. An emerging healthcare application for Nanopore includes point-of-care, timely identification of antibiotic resistance genes (ARGs) to help developing targeted treatments of bacterial infections, and monitoring resistant outbreaks in the environment. While several computational tools exist for classifying ARGs from sequencing data, to date (2022) none have been developed for mobile devices. We present here KARGAMobile, a mobile app for portable, real-time, easily interpretable analysis of ARGs from Nanopore sequencing. KARGAMobile is the porting of an existing ARG identification tool named KARGA; it retains the same algorithmic structure, but it is optimized for mobile devices. Specifically, KARGAMobile employs a compressed ARG reference database and different internal data structures to save RAM usage. The KARGAMobile app features a friendly graphical user interface that guides through file browsing, loading, parameter setup, and process execution. More importantly, the output files are post-processed to create visual, printable and shareable reports, aiding users to interpret the ARG findings. The difference in classification performance between KARGAMobile and KARGA is minimal (96.2% vs. 96.9% f-measure on semi-synthetic datasets of 1 million reads with known resistance ground truth). Using real Nanopore experiments, KARGAMobile processes on average 1 GB data every 23-48 min (targeted sequencing - metagenomics), with peak RAM usage below 500MB, independently from input file sizes, and an average temperature of 49°C after 1 h of continuous data processing. KARGAMobile is written in Java and is available at https://github.com/Ruiz-HCI-Lab/KargaMobile under the MIT license.

A literature review of dispersal pathways of Aedes albopictus across different spatial scales: implications for vector surveillance

BACKGROUND

Aedes albopictus is a highly invasive species and an important vector of dengue and chikungunya viruses. Indigenous to Southeast Asia, Ae. albopictus has successfully invaded every inhabited continent, except Antarctica, in the past 80 years. Vector surveillance and control at points of entry (PoE) is the most critical front line of defence against the introduction of Ae. albopictus to new areas. Identifying the pathways by which Ae. albopictus are introduced is the key to implementing effective vector surveillance to rapidly detect introductions and to eliminate them.

METHODS

A literature review was conducted to identify studies and data sources reporting the known and suspected dispersal pathways of human-mediated Ae. albopictus dispersal between 1940-2020. Studies and data sources reporting the first introduction of Ae. albopictus in a new country were selected for data extraction and analyses.

RESULTS

Between 1940-2020, Ae. albopictus was reported via various dispersal pathways into 86 new countries. Two main dispersal pathways were identified: (1) at global and continental spatial scales, maritime sea transport was the main dispersal pathway for Ae. albopictus into new countries in the middle to late 20th Century, with ships carrying used tyres of particular importance during the 1980s and 1990s, and (2) at continental and national spatial scales, the passive transportation of Ae. albopictus in ground vehicles and to a lesser extent the trade of used tyres and maritime sea transport appear to be the major drivers of Ae. albopictus dispersal into new countries, especially in Europe. Finally, the dispersal pathways for the introduction and spread of Ae. albopictus in numerous countries remains unknown, especially from the 1990s onwards.

CONCLUSIONS

This review identified the main known and suspected dispersal pathways of human-mediated Ae. albopictus dispersal leading to the first introduction of Ae. albopictus into new countries and highlighted gaps in our understanding of Ae. albopictus dispersal pathways. Relevant advances in vector surveillance and genomic tracking techniques are presented and discussed in the context of improving vector surveillance.

Metagenomics-enabled microbial surveillance

Lessons learnt from the COVID-19 pandemic include increased awareness of the potential for zoonoses and emerging infectious diseases that can adversely affect human health. Although emergent viruses are currently in the spotlight, we must not forget the ongoing toll of morbidity and mortality owing to antimicrobial resistance in bacterial pathogens and to vector-borne, foodborne and waterborne diseases. Population growth, planetary change, international travel and medical tourism all contribute to the increasing frequency of infectious disease outbreaks. Surveillance is therefore of crucial importance, but the diversity of microbial pathogens, coupled with resource-intensive methods, compromises our ability to scale-up such efforts. Innovative technologies that are both easy to use and able to simultaneously identify diverse microorganisms (viral, bacterial or fungal) with precision are necessary to enable informed public health decisions. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.

Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects

DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed.

Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.

A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting

Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.

A Cross-Disciplinary View of Testing and Bioinformatic Analysis of SARS-CoV-2 and Other Human Respiratory Viruses in Pandemic Settings

The SARS-Coronavirus-2 (SARS-CoV-2) infectious disease, COVID-19, has spread rapidly, resulting in a global pandemic with significant mortality. The combination of early diagnosis via rapid screening, contact tracing, social distancing and quarantine has helped to control the pandemic. The absence of real time response and diagnosis is a crucial technology shortfall and is a key reason why current contact tracing methods are inadequate to control spread. In contrast, current information technology combined with a new generation of near-real time tests offers consumer-engaged smartphone-based "lab-in-a-phone" internet-of-things (IoT) connected devices that provide increased pandemic monitoring. This review brings together key aspects required to create an entire global diagnostic ecosystem. Cross-disciplinary understanding and integration of both mechanisms and technologies for effective detection, incidence mapping and disease containment in near real-time is summarized. Available measures to monitor and/or sterilize surfaces, next-generation laboratory and smartphone-based diagnostic approaches can be brought together and networked for instant global monitoring that informs Public Health policy. Cloud-based analysis enabling real-time mapping will enable future pandemic control, drive the suppression and elimination of disease spread, saving millions of lives globally. A new paradigm is introduced - scaled and multiple diagnostics for mapping and spreading of a pandemic rather than traditional accumulation of individual measurements. This can do away with the need for ultra-precise and ultra-accurate analysis by taking mass measurements that can relax tolerances and build resilience through networked analytics and informatics, the basis for novel swarm diagnostics. These include addressing ethical standards, local, national and international collaborative engagement, multidisciplinary and analytical measurements and standards, and data handling and storage protocols.

iGenomics: Comprehensive DNA sequence analysis on your Smartphone

BACKGROUND

Following the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is on a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in remote stations around the world. However, despite the simplicity of the sequencer, an equally simple and portable analysis platform is not yet available.

RESULTS

iGenomics is the first comprehensive mobile genome analysis application, with capabilities to align reads, call variants, and visualize the results entirely on an iOS device. Implemented in Objective-C using the FM-index, banded dynamic programming, and other high-performance bioinformatics techniques, iGenomics is optimized to run in a mobile environment. We benchmark iGenomics using a variety of real and simulated Nanopore sequencing datasets of viral and bacterial genomes and show that iGenomics has performance comparable to the popular BWA-MEM/SAMtools/IGV suite, without necessitating a laptop or server cluster.

CONCLUSIONS

iGenomics is available open source (https://github.com/stuckinaboot/iGenomics) and for free on Apple's App Store (https://apple.co/2HCplzr).