KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
Identifieur interne : 000F12 ( PubMed/Corpus ); précédent : 000F11; suivant : 000F13KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
Auteurs : Daniel Mapleson ; Gonzalo Garcia Accinelli ; George Kettleborough ; Jonathan Wright ; Bernardo J. ClavijoSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2017.
English descriptors
- KwdEn :
- MESH :
- genetics : Fraxinus.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
- standards : High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
- Genome, Plant, Quality Control, Software.
Abstract
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.
DOI: 10.1093/bioinformatics/btw663
PubMed: 27797770
Links to Exploration step
pubmed:27797770Le document en format XML
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<author><name sortKey="Mapleson, Daniel" sort="Mapleson, Daniel" uniqKey="Mapleson D" first="Daniel" last="Mapleson">Daniel Mapleson</name>
<affiliation><nlm:affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</nlm:affiliation>
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<author><name sortKey="Garcia Accinelli, Gonzalo" sort="Garcia Accinelli, Gonzalo" uniqKey="Garcia Accinelli G" first="Gonzalo" last="Garcia Accinelli">Gonzalo Garcia Accinelli</name>
<affiliation><nlm:affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</nlm:affiliation>
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<author><name sortKey="Kettleborough, George" sort="Kettleborough, George" uniqKey="Kettleborough G" first="George" last="Kettleborough">George Kettleborough</name>
<affiliation><nlm:affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</nlm:affiliation>
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<author><name sortKey="Wright, Jonathan" sort="Wright, Jonathan" uniqKey="Wright J" first="Jonathan" last="Wright">Jonathan Wright</name>
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<author><name sortKey="Clavijo, Bernardo J" sort="Clavijo, Bernardo J" uniqKey="Clavijo B" first="Bernardo J" last="Clavijo">Bernardo J. Clavijo</name>
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<author><name sortKey="Garcia Accinelli, Gonzalo" sort="Garcia Accinelli, Gonzalo" uniqKey="Garcia Accinelli G" first="Gonzalo" last="Garcia Accinelli">Gonzalo Garcia Accinelli</name>
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<author><name sortKey="Kettleborough, George" sort="Kettleborough, George" uniqKey="Kettleborough G" first="George" last="Kettleborough">George Kettleborough</name>
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<author><name sortKey="Wright, Jonathan" sort="Wright, Jonathan" uniqKey="Wright J" first="Jonathan" last="Wright">Jonathan Wright</name>
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<author><name sortKey="Clavijo, Bernardo J" sort="Clavijo, Bernardo J" uniqKey="Clavijo B" first="Bernardo J" last="Clavijo">Bernardo J. Clavijo</name>
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<series><title level="j">Bioinformatics (Oxford, England)</title>
<idno type="eISSN">1367-4811</idno>
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<term>Genome, Plant</term>
<term>High-Throughput Nucleotide Sequencing (methods)</term>
<term>High-Throughput Nucleotide Sequencing (standards)</term>
<term>Quality Control</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Sequence Analysis, DNA (standards)</term>
<term>Software</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fraxinus</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term>
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<front><div type="abstract" xml:lang="en">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.</div>
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<DateCompleted><Year>2017</Year>
<Month>10</Month>
<Day>18</Day>
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<DateRevised><Year>2018</Year>
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<PubDate><Year>2017</Year>
<Month>02</Month>
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<Title>Bioinformatics (Oxford, England)</Title>
<ISOAbbreviation>Bioinformatics</ISOAbbreviation>
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<ArticleTitle>KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.</ArticleTitle>
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<Abstract><AbstractText Label="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 utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies.</AbstractText>
<AbstractText Label="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.</AbstractText>
<AbstractText Label="Availability and Implementation">KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT .</AbstractText>
<AbstractText Label="Contact">bernardo.clavijo@earlham.ac.uk.</AbstractText>
<AbstractText Label="Supplementary information">Supplementary data are available at Bioinformatics online.</AbstractText>
<CopyrightInformation>© The Author 2016. Published by Oxford University Press.</CopyrightInformation>
</Abstract>
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