标题： Sam2bam：高性能的NGS数据预处理工具框架 显示英文标题

标题： Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

摘要： 本文介绍了一种名为{\it sam2bam}的高吞吐量软件工具框架，该框架使用户能够显著加速下一代测序数据的预处理。 sam2bam 在单节点多核大内存系统上特别高效。 与事实上的标准工具相比，它可以在单节点系统上将标记重复读数的数据预处理运行时间减少 156-186 倍。 sam2bam 包含并行软件组件，可以充分利用多个处理器、可用内存、存储的高带宽以及可用的硬件压缩加速器。 sam2bam 提供了在知名基因组文件格式之间进行文件格式转换的基本功能，例如从 SAM 到 BAM。 {\it 插件}工具提供了诸如分析、过滤和转换输入数据等附加功能，例如重复标记，这些功能可以在运行时附加到 sam2bam 上。 我们证明了在使用最多 130 GB 内存的 16 核单节点系统上，sam2bam 可以将全外显子数据集的 NGS 数据预处理运行时间从大约两个小时减少到大约一分钟。 在使用最多 711 GB 内存的同一系统上，sam2bam 可以将全基因组测序数据的运行时间从大约 20 小时减少到大约九分钟。 显示英文摘要

摘要： 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.