Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples of diverse ancestry. Our analysis shows that Paragraph has better accuracy than other existing genotypers and can be applied to population-scale studies.
Abstract. With the integration of everyday objects and sensors into the Internet, users gain new possibilities to directly interact with their environment. This integration is facilitated by the development of tiny IP stacks that enable a direct Internet connection for resource constrained devices. To provide users with the same level of usability that is predominant in the current Internet infrastructure, a self-configured discovery service for sensors and objects is needed. We thus present a use case of a discovery service based on Multicast DNS and DNS Service Discovery, which we adopt for resource constrained devices and operating systems. Applications using this service can realize direct connections between resource constrained devices following the end-to-end principle of the IP-based Internet, allowing for a seamless integration of potentially millions of objects and sensors into the current Internet and facilitating the pervasive infrastructure that is envisioned by the Internet of Things.
The Internet of Things vision states that sensors and actuators shall be integrated into the global Internet to facilitate an interaction with and integration of the physical environment. The development of enabling technologies like uIPv6 and 6LoWPAN provide the basic requirements for this interconnection. However, a seamless Internet-connection and interconnection between sensors and actuators can still only be provided with the help of protocols that use gateways, intermediate proxies, and protocol translators. We propose a solution to unify the world of sensors and actuators with the Internet through the use of the Extensible Messaging and Presence Protocol (XMPP) while omitting application protocol gateways and protocol translators at the same time. This article describes our ideas to boost the Internet of Things vision by using XMPP. We present our current work in progress and an outlook into our future working directions in this field.
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An important challenge for the Internet of Things is the gap between scientific environments and real life deployments. Smart objects need to be accessible and usable by ordinary users through familiar software and access technologies to facilitate any interaction and to increase their acceptance rate. This work deals with a seamless integration, discovery, and employment of smart objects into the Internet infrastructure under Human-to-Machine (H2M) communication aspects. We introduce an XMPP-based service provisioning sublayer for the IoT to integrate resource constrained devices seamlessly into the Internet by showing how XMPP can empower the collaboration between humans and smart objects. To meet the requirements of constrained devices, we propose to extend XMPP's publish-subscribe capabilities with a topic-based filter mechanism to effectively reduce the number of exchanged XMPP messages. We further present standardized bootstrapping and handling processes for smart objects that adapt automatically to infrastructure and ad hoc network environments and do not require predefined parameters or user interaction. The applicability of XMPP for constrained devices is further demonstrated with an XMPP client and mDNS/DNS-SD service for the Contiki operating system.
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