Kraken: a set of tools for quality control and analysis of high-throughput sequence data.
Kraken: a set of tools for quality control and analysis of high-throughput sequence data.
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DOI：
10.1016/j.ymeth.2013.06.027
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发表时间：
2013-09-01
期刊：
影响因子：
4.8
通讯作者：
Enright, Anton J.
中科院分区：
文献类型：
--
作者：
Davis, Matthew P. A.;van Dongen, Stijn;Abreu-Goodger, Cei;Bartonicek, Nenad;Enright, Anton J.
新的测序技术在数据复杂性和规模方面提出了重大挑战。重要的是，开发出的高效软件的性能与序列信息的增长成比例。在这里，我们提出了一个全面的和综合的一套工具，从大规模测序实验的数据分析。它支持适配器检测和去除、条形码的解复用、双端数据、一系列读取架构以及有效去除序列冗余。序列可以根据长度、质量和复杂性进行修剪和过滤。质量控制图跟踪序列长度、组成和关于基因组注释的汇总统计。多个用例已集成到一个简化的管道中，包括mRNA和小RNA测序实验。该管道与现有的基因组定位和差异表达分析工具相结合。
New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments. It supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy. Sequences can be trimmed and filtered based on length, quality and complexity. Quality control plots track sequence length, composition and summary statistics with respect to genomic annotation. Several use cases have been integrated into a single streamlined pipeline, including both mRNA and small RNA sequencing experiments. This pipeline interfaces with existing tools for genomic mapping and differential expression analysis.
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