KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
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DOI：
10.1093/bioinformatics/btw663
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发表时间：
2017-02-15
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影响因子：
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通讯作者：
Clavijo BJ
中科院分区：
文献类型：
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作者：
Mapleson D;Garcia Accinelli G;Kettleborough G;Wright J;Clavijo BJ
全基因组鸟枪法（WGS）下一代测序（NGS）数据的从头组装受益于高覆盖率的高质量输入。然而，在实践中，以无参考的方式快速确定有用读数的质量和数量并不是微不足道的。更好地了解WGS数据以及装配人员如何利用这些数据，可以提供有用的见解，从而为装配过程提供信息，并产生更好的装配。我们提出了K-mer分析工具包（KAT）：一个多用途的软件工具包，用于WGS读取和从头基因组组装的无参考质量控制（QC），主要是通过其k-mer频率和GC组成。KAT使用户能够评估装配过程各个阶段的错误、偏差和污染程度。在本文中，我们强调KAT的能力，提供有价值的见解组装的组成和质量的基因组组件，通过成对比较的k-mer存在于两个输入读取和组件。KAT可以在GPL v3许可证下获得，网址为：https://github.com/TGAC/KAT。 补充数据可在Bioinformatics在线获得。
De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT’s ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT. Supplementary data are available at Bioinformatics online.