KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
Identifieur interne : 001827 ( Ncbi/Checkpoint ); précédent : 001826; suivant : 001828KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
Auteurs : Daniel Mapleson [Royaume-Uni] ; Gonzalo Garcia Accinelli [Royaume-Uni] ; George Kettleborough [Royaume-Uni] ; Jonathan Wright [Royaume-Uni] ; Bernardo J. Clavijo [Royaume-Uni]Source :
- Bioinformatics [ 1367-4803 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
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
We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and
KAT is available under the GPLv3 license at:
Url:
DOI: 10.1093/bioinformatics/btw663
PubMed: 27797770
PubMed Central: 5408915
Affiliations:
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Clavijo</name><affiliation wicri:level="1"><nlm:aff id="btw663-aff1">Earlham Institute, Norwich Research Park, Norwich, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Earlham Institute, Norwich Research Park, Norwich</wicri:regionArea><wicri:noRegion>Norwich</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1367-4811</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Fraxinus (genetics)</term><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></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Analyse de séquence d'ADN (normes)</term><term>Contrôle de qualité</term><term>Fraxinus (génétique)</term><term>Génome végétal</term><term>Logiciel</term><term>Séquençage nucléotidique à haut débit ()</term><term>Séquençage nucléotidique à haut débit (normes)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fraxinus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Fraxinus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Séquençage nucléotidique à haut débit</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><term>Quality Control</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Contrôle de qualité</term><term>Génome végétal</term><term>Logiciel</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><sec id="SA1"><title>Motivation</title><p><italic>De novo</italic> 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.</p></sec><sec id="SA2"><title>Results</title><p>We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and <italic>de novo</italic> 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.</p></sec><sec id="SA3"><title>Availability and Implementation</title><p>KAT is available under the GPLv3 license at: <ext-link ext-link-type="uri" xlink:href="https://github.com/TGAC/KAT">https://github.com/TGAC/KAT</ext-link>.</p></sec><sec id="SA4"><title>Supplementary information</title><p><xref ref-type="supplementary-material" rid="sup1">Supplementary data</xref> are available at <italic>Bioinformatics</italic> online.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Anvar, S Y" uniqKey="Anvar S">S.Y. Anvar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chor, B" uniqKey="Chor B">B. Chor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lo, C C" uniqKey="Lo C">C.C. Lo</name></author><author><name sortKey="Chain, P S G" uniqKey="Chain P">P.S.G. Chain</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G. Marçais</name></author><author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C. Kingsford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Metzker, M L" uniqKey="Metzker M">M.L. Metzker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schatz, M C" uniqKey="Schatz M">M.C. Schatz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simpson, J T" uniqKey="Simpson J">J.T. Simpson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, X" uniqKey="Yang X">X. Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q. Zhang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Royaume-Uni</li></country></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Mapleson, Daniel" sort="Mapleson, Daniel" uniqKey="Mapleson D" first="Daniel" last="Mapleson">Daniel Mapleson</name></noRegion><name sortKey="Clavijo, Bernardo J" sort="Clavijo, Bernardo J" uniqKey="Clavijo B" first="Bernardo J" last="Clavijo">Bernardo J. Clavijo</name><name sortKey="Garcia Accinelli, Gonzalo" sort="Garcia Accinelli, Gonzalo" uniqKey="Garcia Accinelli G" first="Gonzalo" last="Garcia Accinelli">Gonzalo Garcia Accinelli</name><name sortKey="Kettleborough, George" sort="Kettleborough, George" uniqKey="Kettleborough G" first="George" last="Kettleborough">George Kettleborough</name><name sortKey="Wright, Jonathan" sort="Wright, Jonathan" uniqKey="Wright J" first="Jonathan" last="Wright">Jonathan Wright</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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