BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.
BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing.
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DOI：
10.1186/s12859-018-2262-7
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发表时间：
2018-07-05
影响因子：
3
通讯作者：
Paulin L
中科院分区：
文献类型：
--
作者：
Somervuo P;Koskinen P;Mei P;Holm L;Auvinen P;Paulin L
当前的高通量测序平台提供了并行测序多个样本的能力。通过将短样本特定核苷酸序列（条形码）附加到每个 DNA 分子上来标记不同的样本，然后将它们汇集到包含多个要同时测序的文库的混合物中。测序后，通过识别每个序列读取中的条形码序列来对样品进行分箱。为了容忍测序错误，条形码在序列空间中应彼此充分分开。由于核苷酸使用和碱基识别准确性的另一个限制是每个条形码位置中不同核苷酸的比例应该保持平衡。每次测序运行中混合的样品数量可能会有所不同，这引入了如何在每次测序运行的测序核心设施中选择可用条形码的最佳子集的问题。有很多工具可用于从头条形码设计，但它们不适合子集选择。我们开发了一种工具，可用于三种不同的任务：1）从更大的候选条码集中选择最佳条码集，2）检查用户定义的条码集的兼容性，例如是否可以将两个或多个带有现有条形码的文库合并到一个测序池中，以及 3) 扩充现有的一组条形码。在我们的方法中，选择过程被表述为一个最小化问题。我们定义成本函数和一组约束，并使用整数规划来解决由此产生的组合问题。根据所需选择的条形码数量和用户给出的候选序列集，自动生成必要的约束并找到最佳解决方案。该方法用 C 编程语言实现，Web 界面可在 http://ekhidna2.biocenter.helsinki.fi/barcosel 上获得。测序平台容量的增加提出了混合条形码的挑战。我们的方法允许用户在较大的现有条形码集中选择给定数量的条形码，以便容忍测序错误并优化核苷酸平衡。该工具可以通过网络浏览器轻松访问。本文的在线版本 (10.1186/s12859-018-2262-7) 包含补充材料，可供授权用户使用。
Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read. In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection. We have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes. In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel. Increasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser. The online version of this article (10.1186/s12859-018-2262-7) contains supplementary material, which is available to authorized users.
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影响因子：
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