Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type's strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.

This paper presents a general design for providing access to remote devices, pipes, and FIFOs, within a distributed computing environment. Though the design is presented in terms of SVR4 and Sun ONC, it is sufficiently general to be built upon almost any underlying Unix system and distribution architecture. The design is applicable to all types of devices, and special attention is given to STREAMS oriented devices.>

LOCUS is a distributed operating system which supports transparent access to data through a network wide filesystem, permits automatic replication of storage, supports transparent distributed process execution, supplies a number of high reliability functions such as nested transactions, and is upward compatible with Unix. Partitioned operation of subnet's and their dynamic merge is also supported.

Many distributed systems are now being developed to provide users with convenient access to data via some kind of communications network. In many cases it is desirable to keep the system functioning even when it is partitioned by network failures. A serious problem in this context is how one can support redundant copies of resources such as files (for the sake of reliability) while simultaneously monitoring their mutual consistency (the equality of multiple copies). This is difficult since network faiures can lead to inconsistency, and disrupt attempts at maintaining consistency. In fact, even the detection of inconsistent copies is a nontrivial problem. Naive methods either 1) compare the multiple copies entirely or 2) perform simple tests which will diagnose some consistent copies as inconsistent. Here a new approach, involving version vectors and origin points, is presented and shown to detect single file, multiple copy mutual inconsistency effectively. The approach has been used in the design of LOCUS, a local network operating system at UCLA.

LOCUS is a distributed operating system that provides a very high degree of network transparency while at the same time supporting high performance and automatic replication of storage. By network transparency we mean that at the system call interface there is no need to mention anything network related. Knowledge of the network and code to interact with foreign sites is below this interface and is thus hidden from both users and programs under normal conditions. LOCUS is application code compatible with Unix2, and performance compares favorably with standard, single system Unix. LOCUS runs on a high bandwidth, low delay local network. It is designed to permit both a significant degree of local autonomy for each site in the network while still providing a network-wide, location independent name structure. Atomic file operations and extensive synchronization are supported.

Data Secure Unix, a kernel structured operating system, was constructed as part of an ongoing effort at UCLA to develop procedures by which operating systems can be produced and shown secure. Program verification methods were extensively applied as a constructive means of demonstrating security enforcement.