Updates to the RMAP short-read mapping software.
Updates to the RMAP short-read mapping software.
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DOI：
10.1093/bioinformatics/btp533
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发表时间：
2009-11-01
期刊：
影响因子：
--
通讯作者：
Zhang MQ
中科院分区：
文献类型：
--
作者：
Smith AD;Chung WY;Hodges E;Kendall J;Hannon G;Hicks J;Xuan Z;Zhang MQ
摘要：我们报告了一个主要的新版本的RMAP软件，用于映射来自短读段测序技术的读段。包括对精度和空间要求的一般改进，以及沿着新功能。RMAP软件包中包括用于映射双端读段、使用更复杂的质量评分进行映射、收集模糊映射位置和映射亚硫酸氢盐处理的读段的工具。可用性：本说明中描述的应用程序可在http://www.cmb.usc.edu/people/andrewds/rmap上下载，并作为GPL v3.0下的开放源码软件分发。该软件已在Linux和OS X平台上进行了测试。联系方式：andrewds@usc.edu; mzhang@cshl.edu RMAP算法由（Smith et al.，）作为Illumina第二代测序技术的最早可用程序之一。RMAP的一个重要贡献是将质量分数的使用直接纳入映射过程：在映射时不考虑质量分数过低的读取位置，并且用户可以调整质量分数截止值。随后，出现了许多映射算法（Langmead等人，; Li，H.等，;利河，巴西-地等，; Lin等人，; Schatz; Yanovsky等人），在效率和功能广度（例如，映射双端读段的能力;整合的SNP调用）方面都有改进。需要解决绘图问题的调查人员现在有许多选择。随着短读段测序的新应用的出现，读段作图的分析任务出现了许多变化。现有映射工具的性能特征的多样性变得潜在地有价值。我们报告RMAP的第一个主要更新。RMAP中的基本算法框架仍然是预处理读取和扫描基因组，但已进行了一些修改，并包含了许多额外的功能。重要的是，RMAP的内存占用取决于映射的读取数量。此功能允许在具有商用节点的集群环境中有效使用RMAP，因为对读取进行分区允许自然并行化，从而线性减少每个处理器内核的内存需求。RMAP软件包的此版本中包括用于映射双端读数、更复杂地使用质量评分、收集不明确映射读数的映射位置以及映射亚硫酸氢盐处理的读数的功能。
Summary: We report on a major new version of the RMAP software for mapping reads from short-read sequencing technology. General improvements to accuracy and space requirements are included, along with novel functionality. Included in the RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use of quality scores, collecting ambiguous mapping locations and mapping bisulfite-treated reads. Availability: The applications described in this note are available for download at http://www.cmb.usc.edu/people/andrewds/rmap and are distributed as Open Source software under the GPLv3.0. The software has been tested on Linux and OS X platforms. Contact: andrewds@usc.edu; mzhang@cshl.edu The RMAP algorithm was introduced by (Smith et al.,) as one of the earliest available programs for mapping reads from the Illumina second-generation sequencing technology. One important contribution of RMAP was to incorporate the use of quality scores directly into the mapping process: read positions with too low a quality score were not considered while mapping, and that quality score cutoff could be adjusted by the user. Subsequently, numerous mapping algorithm have appeared (Langmead et al.,; Li,H. et al.,; Li,R. et al.,; Lin et al.,; Schatz,; Yanovsky et al.,), with improvements in both efficiency and breadth of functionality (e.g. ability to map paired-end reads; integrated SNP calling). Investigators requiring solutions to mapping problems now have many options. As new applications of short-read sequencing emerge, many variations on the analysis task of read mapping emerge. Diversity in performance characteristics of existing mapping tools becomes potentially valuable. We report the first major update to RMAP. The basic algorithmic framework in RMAP is still to preprocess reads and scan the genome, but several modifications have been made and much additional functionality has been included. Importantly, RMAP has a memory footprint that depends on the number of reads being mapped. This feature allows RMAP to be used effectively in cluster environments with commodity nodes, because partitioning the reads allows natural parallelizations with linear reduction in memory requirements per processor core used. Included in this release of the RMAP software package is functionality for mapping paired-end reads, making more sophisticated use of quality scores, collecting mapping locations for ambiguously mapping reads and mapping bisulfite-treated reads.
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影响因子：
0.5
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通讯作者：
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