Jul 19, 2016

KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies

BioRxiv : the Preprint Server for Biology
Daniel MaplesonBernardo J. Clavijo


ABSTRACT Motivation: 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 utilised by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. Results: 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. Availability: KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT.

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Mentioned in this Paper

Computer Software
Severe Acute Respiratory Syndrome
Whole-Genome Shotgun Sequencing
Malignant Neoplasm of Stomach
Massively-Parallel Sequencing
Whole Genome Sequencing

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