KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
Identifieur interne : 000C49 ( PubMed/Checkpoint ); précédent : 000C48; suivant : 000C50KAT: 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 (Oxford, England) [ 1367-4811 ] ; 2017.
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
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
Affiliations:
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pubmed:27797770Le document en format XML
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Clavijo</name><affiliation wicri:level="1"><nlm:affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</nlm:affiliation><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 (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2017" type="published">2017</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">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></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">27797770</PMID><DateCompleted><Year>2017</Year><Month>10</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>4</Issue><PubDate><Year>2017</Year><Month>02</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.</ArticleTitle><Pagination><MedlinePgn>574-576</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btw663</ELocationID><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><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mapleson</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Garcia Accinelli</LastName><ForeName>Gonzalo</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kettleborough</LastName><ForeName>George</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wright</LastName><ForeName>Jonathan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Clavijo</LastName><ForeName>Bernardo J</ForeName><Initials>BJ</Initials><AffiliationInfo><Affiliation>Earlham Institute, Norwich Research Park, Norwich, UK.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>BB/J004669/1</GrantID><Agency>Biotechnology and Biological Sciences Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D031661" MajorTopicYN="N">Fraxinus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName><QualifierName UI="Q000592" MajorTopicYN="Y">standards</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011786" MajorTopicYN="Y">Quality Control</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName><QualifierName UI="Q000592" MajorTopicYN="Y">standards</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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IdType="pubmed">23363224</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2010 Jan;11(1):31-46</Citation><ArticleIdList><ArticleId IdType="pubmed">19997069</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2014 May 1;30(9):1228-35</Citation><ArticleIdList><ArticleId IdType="pubmed">24443382</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2014;15(12):555</Citation><ArticleIdList><ArticleId IdType="pubmed">25514851</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Mar 15;27(6):764-70</Citation><ArticleIdList><ArticleId IdType="pubmed">21217122</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2012;13(4):243</Citation><ArticleIdList><ArticleId IdType="pubmed">22546054</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2014 Nov 19;15:366</Citation><ArticleIdList><ArticleId IdType="pubmed">25408143</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2014 Jul 25;9(7):e101271</Citation><ArticleIdList><ArticleId IdType="pubmed">25062443</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2009;10(10):R108</Citation><ArticleIdList><ArticleId IdType="pubmed">19814784</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><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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