Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156-186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize the multiple processors, available memory, high-bandwidth of storage, and hardware compression accelerators if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting the input data are provided by {\it plug-in} tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of NGS data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime for whole-genome sequencing data from about 20 hours to about nine minutes on the same system using up to 711 GB of memory

Beam Loss Monitors at LHC

One of the main functions of the LHC beam loss measurement system is the protection of equipment against damage caused by impacting particles creating secondary showers and their energy dissipation in the matter. Reliability requirements are scaled according to the acceptable consequences and the frequency of particle impact events on equipment. Increasing reliability often leads to more complex systems. The downside of complexity is a reduction of availability; therefore, an optimum has to be found for these conflicting requirements. A detailed review of selected concepts and solutions for the LHC system will be given to show approaches used in various parts of the system from the sensors, signal processing, and software implementations to the requirements for operation and documentation.Comment: 16 pages, contribution to the 2014 Joint International Accelerator School: Beam Loss and Accelerator Protection, Newport Beach, CA, USA , 5-14 Nov 201

Controls and Interfaces

Reliable powering of accelerator magnets requires reliable power converters and controls, able to meet the powering specifications in the long term. In this paper, some of the issues that will challenge a power converter controls engineer are discussed.Comment: 16 pages, contribution to the 2014 CAS - CERN Accelerator School: Power Converters, Baden, Switzerland, 7-14 May 201