PEAR: a fast and accurate Illumina Paired-End reAd mergeR.
PEAR: a fast and accurate Illumina Paired-End reAd mergeR.
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DOI：
10.1093/bioinformatics/btt593
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发表时间：
2014-03-01
期刊：
影响因子：
--
通讯作者：
Stamatakis A
中科院分区：
文献类型：
--
作者：
Zhang J;Kobert K;Flouri T;Stamatakis A
动机：Illumina双端测序技术可以从靶DNA片段的两端产生读段，随后可以将其合并以增加总读段长度。当目标片段等长时，已经存在用于合并这些双端读段的工具。然而，当片段长度变化时，特别是当片段大小短于单端读段或长于单端读段大小的两倍时，大多数最先进的合并无法产生可靠的结果。因此，需要一种稳健的工具来合并由于不同的靶片段长度而表现出不同重叠长度的双端读段。结果：我们提出了PEAR软件，用于合并来自不同长度的靶片段的原始Illumina配对末端读段。该程序评估所有可能的双端读段重叠，并且不需要目标片段大小作为输入。它还实现了统计测试，以最大限度地减少假阳性结果。对模拟和经验数据的测试表明，PEAR始终生成高度准确的合并双端读数。高度优化的实现允许在标准台式计算机上在几分钟内合并数百万个双端读取。在多核架构上，并行版本的PEAR与顺序版本的PEAR相比显示出线性加速。可用性和实现：PEAR是用C实现的，使用POSIX线程。它可以在http://www.exelixis-lab.org/web/software/pear上免费获得。联系人：Tomas. h-its.org
Motivation: The Illumina paired-end sequencing technology can generate reads from both ends of target DNA fragments, which can subsequently be merged to increase the overall read length. There already exist tools for merging these paired-end reads when the target fragments are equally long. However, when fragment lengths vary and, in particular, when either the fragment size is shorter than a single-end read, or longer than twice the size of a single-end read, most state-of-the-art mergers fail to generate reliable results. Therefore, a robust tool is needed to merge paired-end reads that exhibit varying overlap lengths because of varying target fragment lengths. Results: We present the PEAR software for merging raw Illumina paired-end reads from target fragments of varying length. The program evaluates all possible paired-end read overlaps and does not require the target fragment size as input. It also implements a statistical test for minimizing false-positive results. Tests on simulated and empirical data show that PEAR consistently generates highly accurate merged paired-end reads. A highly optimized implementation allows for merging millions of paired-end reads within a few minutes on a standard desktop computer. On multi-core architectures, the parallel version of PEAR shows linear speedups compared with the sequential version of PEAR. Availability and implementation: PEAR is implemented in C and uses POSIX threads. It is freely available at http://www.exelixis-lab.org/web/software/pear. Contact: Tomas.Flouri@h-its.org
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影响因子：
48
作者：
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影响因子：
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作者：
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DOI：
10.1073/pnas.1000080107
发表时间：
2011-03-15
影响因子：
11.1
作者：
Caporaso, J. Gregory;Lauber, Christian L.;Knight, Rob
通讯作者：
Knight, Rob