BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing.
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing.
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DOI：
10.1186/1471-2105-10-362
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发表时间：
2009-10-29
影响因子：
3
通讯作者：
Frank DN
中科院分区：
文献类型：
--
作者：
Frank DN
自动 DNA 测序技术的进步极大地扩大了基因组和宏基因组研究的规模。提高项目通量的一种日益流行的方法是在测序阶段对样本进行多重分析。这可以通过将短的、独特的“条形码”DNA片段与基因组DNA样本共价连接来实现，例如通过在PCR引物中掺入条形码序列。尽管已经描述了几种策略来确保条形码序列独特且对测序错误具有鲁棒性，但这些策略尚未整合到整个引物设计过程中，因此可能会在 PCR 扩增和/或测序步骤中引入偏差。 Barcrawl 是一款软件程序，可促进条形码引物的设计，用于多重高通量测序。 bartab 程序可用于对使用多个条形码引物产生的 DNA 序列数据集进行解卷积。本文描述了 barcrawl 和 bartab 实现的功能，并提出了这两个程序的概念验证案例研究，其中条形码 rRNA 引物是通过高通量测序设计和验证的。 Barcrawl 和 bartab 可以使从事采用多重样本处理的宏基因组项目的研究人员受益。源代码是在 GNU 通用公共许可证下发布的，可以在 访问。
Advances in automated DNA sequencing technology have greatly increased the scale of genomic and metagenomic studies. An increasingly popular means of increasing project throughput is by multiplexing samples during the sequencing phase. This can be achieved by covalently linking short, unique "barcode" DNA segments to genomic DNA samples, for instance through incorporation of barcode sequences in PCR primers. Although several strategies have been described to insure that barcode sequences are unique and robust to sequencing errors, these have not been integrated into the overall primer design process, thus potentially introducing bias into PCR amplification and/or sequencing steps. Barcrawl is a software program that facilitates the design of barcoded primers, for multiplexed high-throughput sequencing. The program bartab can be used to deconvolute DNA sequence datasets produced by the use of multiple barcoded primers. This paper describes the functions implemented by barcrawl and bartab and presents a proof-of-concept case study of both programs in which barcoded rRNA primers were designed and validated by high-throughput sequencing. Barcrawl and bartab can benefit researchers who are engaged in metagenomic projects that employ multiplexed specimen processing. The source code is released under the GNU general public license and can be accessed at .
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