PittsburghV1, Canada, Analysis, bibRecord, 000152

Fast and Accurate Mapping of Complete Genomics Reads

Identifieur interne : 000152 ( Canada/Analysis ); précédent : 000151; suivant : 000153

Fast and Accurate Mapping of Complete Genomics Reads

Auteurs : Donghyuk Lee [États-Unis] ; Farhad Hormozdiari [États-Unis] ; Hongyi Xin [États-Unis] ; Faraz Hach [Canada] ; Onur Mutlu [États-Unis] ; Can Alkan [Turquie]

Source :

Methods (San Diego, Calif.) [ 1046-2023 ] ; 2014.

RBID : PMC:4406782

Descripteurs français

KwdFr :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Génome humain, Génomique (), Humains, Logiciel, Séquençage nucléotidique à haut débit, Traitement automatique des données ().
MESH :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Génome humain, Génomique, Humains, Logiciel, Séquençage nucléotidique à haut débit, Traitement automatique des données.

English descriptors

KwdEn :
- Algorithms, Automatic Data Processing (methods), Genome, Human, Genomics (methods), High-Throughput Nucleotide Sequencing, Humans, Sequence Alignment, Sequence Analysis, DNA, Software.
MESH :
- methods : Automatic Data Processing, Genomics.
- Algorithms, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Sequence Alignment, Sequence Analysis, DNA, Software.

Abstract

Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of different sequencing technologies currently available, and each HTS platform have different strengths and biases. This diversity both makes it possible to use different technologies to correct for shortcomings; but also requires to develop different algorithms for each platform due to the differences in data types and error models. The first problem to tackle in analyzing HTS data for resequencing applications is the read mapping stage, where many tools have been developed for the most popular HTS methods, but publicly available and open source aligners are still lacking for the Complete Genomics (CG) platform. Unfortunately, Burrows-Wheeler based methods are not practical for CG data due to the gapped nature of the reads generated by this method. Here we provide a sensitive read mapper (sirFAST) for the CG technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome. We evaluate the performance and accuracy of sirFAST using both simulated and publicly available real data sets, showing high precision and recall rates.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406782

DOI: 10.1016/j.ymeth.2014.10.012
PubMed: 25461772
PubMed Central: 4406782

Affiliations:

Links to Exploration step

PMC:4406782

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Fast and Accurate Mapping of Complete Genomics Reads</title>
<author><name sortKey="Lee, Donghyuk" sort="Lee, Donghyuk" uniqKey="Lee D" first="Donghyuk" last="Lee">Donghyuk Lee</name>
<affiliation wicri:level="4"><nlm:aff id="A1">Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université Carnegie-Mellon</orgName>
</affiliation>
</author>
<author><name sortKey="Hormozdiari, Farhad" sort="Hormozdiari, Farhad" uniqKey="Hormozdiari F" first="Farhad" last="Hormozdiari">Farhad Hormozdiari</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science, University of California Los Angeles, Los Angeles, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Xin, Hongyi" sort="Xin, Hongyi" uniqKey="Xin H" first="Hongyi" last="Xin">Hongyi Xin</name>
<affiliation wicri:level="4"><nlm:aff id="A1">Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université Carnegie-Mellon</orgName>
</affiliation>
</author>
<author><name sortKey="Hach, Faraz" sort="Hach, Faraz" uniqKey="Hach F" first="Faraz" last="Hach">Faraz Hach</name>
<affiliation wicri:level="1"><nlm:aff id="A3">School of Computing Science, Simon Fraser University, Burnaby, BC, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>School of Computing Science, Simon Fraser University, Burnaby, BC</wicri:regionArea>
<wicri:noRegion>BC</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mutlu, Onur" sort="Mutlu, Onur" uniqKey="Mutlu O" first="Onur" last="Mutlu">Onur Mutlu</name>
<affiliation wicri:level="4"><nlm:aff id="A1">Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université Carnegie-Mellon</orgName>
</affiliation>
</author>
<author><name sortKey="Alkan, Can" sort="Alkan, Can" uniqKey="Alkan C" first="Can" last="Alkan">Can Alkan</name>
<affiliation wicri:level="1"><nlm:aff id="A4">Department of Computer Engineering, Bilkent University, Ankara, Turkey</nlm:aff>
<country xml:lang="fr">Turquie</country>
<wicri:regionArea>Department of Computer Engineering, Bilkent University, Ankara</wicri:regionArea>
<wicri:noRegion>Ankara</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25461772</idno>
<idno type="pmc">4406782</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406782</idno>
<idno type="RBID">PMC:4406782</idno>
<idno type="doi">10.1016/j.ymeth.2014.10.012</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">001867</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001867</idno>
<idno type="wicri:Area/Pmc/Curation">001842</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001842</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001330</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001330</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="wicri:Area/PubMed/Corpus">000245</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000245</idno>
<idno type="wicri:Area/PubMed/Curation">000245</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000245</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000245</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000245</idno>
<idno type="wicri:Area/Ncbi/Merge">004205</idno>
<idno type="wicri:Area/Ncbi/Curation">004205</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">004205</idno>
<idno type="wicri:doubleKey">1046-2023:2014:Lee D:fast:and:accurate</idno>
<idno type="wicri:Area/Main/Merge">002F47</idno>
<idno type="wicri:Area/Main/Curation">002E13</idno>
<idno type="wicri:Area/Main/Exploration">002E13</idno>
<idno type="wicri:Area/Canada/Extraction">000152</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Fast and Accurate Mapping of Complete Genomics Reads</title>
<author><name sortKey="Lee, Donghyuk" sort="Lee, Donghyuk" uniqKey="Lee D" first="Donghyuk" last="Lee">Donghyuk Lee</name>
<affiliation wicri:level="4"><nlm:aff id="A1">Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université Carnegie-Mellon</orgName>
</affiliation>
</author>
<author><name sortKey="Hormozdiari, Farhad" sort="Hormozdiari, Farhad" uniqKey="Hormozdiari F" first="Farhad" last="Hormozdiari">Farhad Hormozdiari</name>
<affiliation wicri:level="2"><nlm:aff id="A2">Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science, University of California Los Angeles, Los Angeles, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Xin, Hongyi" sort="Xin, Hongyi" uniqKey="Xin H" first="Hongyi" last="Xin">Hongyi Xin</name>
<affiliation wicri:level="4"><nlm:aff id="A1">Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université Carnegie-Mellon</orgName>
</affiliation>
</author>
<author><name sortKey="Hach, Faraz" sort="Hach, Faraz" uniqKey="Hach F" first="Faraz" last="Hach">Faraz Hach</name>
<affiliation wicri:level="1"><nlm:aff id="A3">School of Computing Science, Simon Fraser University, Burnaby, BC, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>School of Computing Science, Simon Fraser University, Burnaby, BC</wicri:regionArea>
<wicri:noRegion>BC</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Mutlu, Onur" sort="Mutlu, Onur" uniqKey="Mutlu O" first="Onur" last="Mutlu">Onur Mutlu</name>
<affiliation wicri:level="4"><nlm:aff id="A1">Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
<settlement type="city">Pittsburgh</settlement>
</placeName>
<orgName type="university">Université Carnegie-Mellon</orgName>
</affiliation>
</author>
<author><name sortKey="Alkan, Can" sort="Alkan, Can" uniqKey="Alkan C" first="Can" last="Alkan">Can Alkan</name>
<affiliation wicri:level="1"><nlm:aff id="A4">Department of Computer Engineering, Bilkent University, Ankara, Turkey</nlm:aff>
<country xml:lang="fr">Turquie</country>
<wicri:regionArea>Department of Computer Engineering, Bilkent University, Ankara</wicri:regionArea>
<wicri:noRegion>Ankara</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Methods (San Diego, Calif.)</title>
<idno type="ISSN">1046-2023</idno>
<idno type="eISSN">1095-9130</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Automatic Data Processing (methods)</term>
<term>Genome, Human</term>
<term>Genomics (methods)</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
<term>Génome humain</term>
<term>Génomique ()</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Traitement automatique des données ()</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Automatic Data Processing</term>
<term>Genomics</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Genome, Human</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
<term>Génome humain</term>
<term>Génomique</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Traitement automatique des données</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p id="P2">Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of different sequencing technologies currently available, and each HTS platform have different strengths and biases. This diversity both makes it possible to use different technologies to correct for shortcomings; but also requires to develop different algorithms for each platform due to the differences in data types and error models. The first problem to tackle in analyzing HTS data for resequencing applications is the read mapping stage, where many tools have been developed for the most popular HTS methods, but publicly available and open source aligners are still lacking for the Complete Genomics (CG) platform. Unfortunately, Burrows-Wheeler based methods are not practical for CG data due to the gapped nature of the reads generated by this method. Here we provide a sensitive read mapper (sirFAST) for the CG technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome. We evaluate the performance and accuracy of sirFAST using both simulated and publicly available real data sets, showing high precision and recall rates.</p>
</div>
</front>
</TEI>
<affiliations><list><country><li>Canada</li>
<li>Turquie</li>
<li>États-Unis</li>
</country>
<region><li>Californie</li>
<li>Pennsylvanie</li>
</region>
<settlement><li>Pittsburgh</li>
</settlement>
<orgName><li>Université Carnegie-Mellon</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Lee, Donghyuk" sort="Lee, Donghyuk" uniqKey="Lee D" first="Donghyuk" last="Lee">Donghyuk Lee</name>
</region>
<name sortKey="Hormozdiari, Farhad" sort="Hormozdiari, Farhad" uniqKey="Hormozdiari F" first="Farhad" last="Hormozdiari">Farhad Hormozdiari</name>
<name sortKey="Mutlu, Onur" sort="Mutlu, Onur" uniqKey="Mutlu O" first="Onur" last="Mutlu">Onur Mutlu</name>
<name sortKey="Xin, Hongyi" sort="Xin, Hongyi" uniqKey="Xin H" first="Hongyi" last="Xin">Hongyi Xin</name>
</country>
<country name="Canada"><noRegion><name sortKey="Hach, Faraz" sort="Hach, Faraz" uniqKey="Hach F" first="Faraz" last="Hach">Faraz Hach</name>
</noRegion>
</country>
<country name="Turquie"><noRegion><name sortKey="Alkan, Can" sort="Alkan, Can" uniqKey="Alkan C" first="Can" last="Alkan">Can Alkan</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Amérique/explor/PittsburghV1/Data/Canada/Analysis

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000152 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Canada/Analysis/biblio.hfd -nk 000152 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Amérique
   |area=    PittsburghV1
   |flux=    Canada
   |étape=   Analysis
   |type=    RBID
   |clé=     PMC:4406782
   |texte=   Fast and Accurate Mapping of Complete Genomics Reads
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Canada/Analysis/RBID.i   -Sk "pubmed:25461772" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Canada/Analysis/biblio.hfd   \
       | NlmPubMed2Wicri -a PittsburghV1

This area was generated with Dilib version V0.6.38.
Data generation: Fri Jun 18 17:37:45 2021. Site generation: Fri Jun 18 18:15:47 2021

Serveur d'exploration sur Pittsburgh

Fast and Accurate Mapping of Complete Genomics Reads

Fast and Accurate Mapping of Complete Genomics Reads

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration sur Pittsburgh
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.