MOTIVATION: Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol uses a circularization-based strategy that leaves behind 38-bp adapter sequences, which must be computationally removed from the data. While 'adapter trimming' is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary. RESULTS: We present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. NxTrim makes full use of the sequence on both sides of the adapter site to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads. For bacterial data, we show that aggregating these datasets allows a single NMP library to yield an assembly whose quality compares favourably to that obtained from regular paired-end reads. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/sequencing/NxTrim

Due to the similar properties of wired and wireless communication systems, it is often possible to adopt established communication principles from one system to another. However, there is one unique property of the wireless channel which differs greatly from its wired counterpart - the transmission signal is gradually decaying beyond recognition. Considering this difference in view of wireless multi-hop networks requires a change of transmission protection. In this paper the authors propose a novel approach which protects the n-hop neighborhood around the receiver. Our study includes a formal analysis of this approach, provides further insights by simulations, and compares it to current protocols. The results demonstrate that our scheme produces higher throughput with significantly lower PER than RTS/CTS-based systems. Furthermore, the performance of our n-hop receiver protection is more stable when confronted with changes in packet size and density of nodes which is severely degraded when RTS/CTS is in use.

This paper presents an end-to-end reservation protocol for quality-of-service (QoS) support in the medium access control layer of wireless multihop mesh networks. It reserves periodically repeating time slots for QoS-demanding applications, while retaining the distributed coordination function (DCF) for best effort applications. The key features of the new protocol, called "distributed end-to-end allocation of time slots for real-time traffic (DARE), are distributed setup, interference protection, and scheduling of real-time data packets, as well as the repair of broken reservations and the release of unused reservations. A simulation-based performance study compares the delay and throughput of DARE with those of DCF and the priority-based enhanced distributed channel access (EDCA) used in IEEE 802.11e. In contrast to DCF and EDCA, DARE has a low, nonvarying delay and a constant throughput for each reserved flow