Konnector v2.0: pseudo-long reads from paired-end sequencing data.
Identifieur interne : 001494 ( PubMed/Checkpoint ); précédent : 001493; suivant : 001495Konnector v2.0: pseudo-long reads from paired-end sequencing data.
Auteurs : Benjamin P. Vandervalk ; Chen Yang ; Zhuyi Xue ; Karthika Raghavan ; Justin Chu ; Hamid Mohamadi ; Shaun D. Jackman ; Readman Chiu ; René L. Warren ; Inanç BirolSource :
- BMC medical genomics [ 1755-8794 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- methods : Sequence Analysis, DNA.
- Algorithms, High-Throughput Nucleotide Sequencing, Software.
Abstract
Reading the nucleotides from two ends of a DNA fragment is called paired-end tag (PET) sequencing. When the fragment length is longer than the combined read length, there remains a gap of unsequenced nucleotides between read pairs. If the target in such experiments is sequenced at a level to provide redundant coverage, it may be possible to bridge these gaps using bioinformatics methods. Konnector is a local de novo assembly tool that addresses this problem. Here we report on version 2.0 of our tool.
DOI: 10.1186/1755-8794-8-S3-S1
PubMed: 26399504
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:26399504Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Konnector v2.0: pseudo-long reads from paired-end sequencing data.</title><author><name sortKey="Vandervalk, Benjamin P" sort="Vandervalk, Benjamin P" uniqKey="Vandervalk B" first="Benjamin P" last="Vandervalk">Benjamin P. Vandervalk</name></author><author><name sortKey="Yang, Chen" sort="Yang, Chen" uniqKey="Yang C" first="Chen" last="Yang">Chen Yang</name></author><author><name sortKey="Xue, Zhuyi" sort="Xue, Zhuyi" uniqKey="Xue Z" first="Zhuyi" last="Xue">Zhuyi Xue</name></author><author><name sortKey="Raghavan, Karthika" sort="Raghavan, Karthika" uniqKey="Raghavan K" first="Karthika" last="Raghavan">Karthika Raghavan</name></author><author><name sortKey="Chu, Justin" sort="Chu, Justin" uniqKey="Chu J" first="Justin" last="Chu">Justin Chu</name></author><author><name sortKey="Mohamadi, Hamid" sort="Mohamadi, Hamid" uniqKey="Mohamadi H" first="Hamid" last="Mohamadi">Hamid Mohamadi</name></author><author><name sortKey="Jackman, Shaun D" sort="Jackman, Shaun D" uniqKey="Jackman S" first="Shaun D" last="Jackman">Shaun D. Jackman</name></author><author><name sortKey="Chiu, Readman" sort="Chiu, Readman" uniqKey="Chiu R" first="Readman" last="Chiu">Readman Chiu</name></author><author><name sortKey="Warren, Rene L" sort="Warren, Rene L" uniqKey="Warren R" first="René L" last="Warren">René L. Warren</name></author><author><name sortKey="Birol, Inanc" sort="Birol, Inanc" uniqKey="Birol I" first="Inanç" last="Birol">Inanç Birol</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26399504</idno><idno type="pmid">26399504</idno><idno type="doi">10.1186/1755-8794-8-S3-S1</idno><idno type="wicri:Area/PubMed/Corpus">001461</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001461</idno><idno type="wicri:Area/PubMed/Curation">001461</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001461</idno><idno type="wicri:Area/PubMed/Checkpoint">001494</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001494</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Konnector v2.0: pseudo-long reads from paired-end sequencing data.</title><author><name sortKey="Vandervalk, Benjamin P" sort="Vandervalk, Benjamin P" uniqKey="Vandervalk B" first="Benjamin P" last="Vandervalk">Benjamin P. Vandervalk</name></author><author><name sortKey="Yang, Chen" sort="Yang, Chen" uniqKey="Yang C" first="Chen" last="Yang">Chen Yang</name></author><author><name sortKey="Xue, Zhuyi" sort="Xue, Zhuyi" uniqKey="Xue Z" first="Zhuyi" last="Xue">Zhuyi Xue</name></author><author><name sortKey="Raghavan, Karthika" sort="Raghavan, Karthika" uniqKey="Raghavan K" first="Karthika" last="Raghavan">Karthika Raghavan</name></author><author><name sortKey="Chu, Justin" sort="Chu, Justin" uniqKey="Chu J" first="Justin" last="Chu">Justin Chu</name></author><author><name sortKey="Mohamadi, Hamid" sort="Mohamadi, Hamid" uniqKey="Mohamadi H" first="Hamid" last="Mohamadi">Hamid Mohamadi</name></author><author><name sortKey="Jackman, Shaun D" sort="Jackman, Shaun D" uniqKey="Jackman S" first="Shaun D" last="Jackman">Shaun D. Jackman</name></author><author><name sortKey="Chiu, Readman" sort="Chiu, Readman" uniqKey="Chiu R" first="Readman" last="Chiu">Readman Chiu</name></author><author><name sortKey="Warren, Rene L" sort="Warren, Rene L" uniqKey="Warren R" first="René L" last="Warren">René L. Warren</name></author><author><name sortKey="Birol, Inanc" sort="Birol, Inanc" uniqKey="Birol I" first="Inanç" last="Birol">Inanç Birol</name></author></analytic><series><title level="j">BMC medical genomics</title><idno type="eISSN">1755-8794</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>DNA (chemistry)</term><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Logiciel</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>High-Throughput Nucleotide Sequencing</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Logiciel</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Reading the nucleotides from two ends of a DNA fragment is called paired-end tag (PET) sequencing. When the fragment length is longer than the combined read length, there remains a gap of unsequenced nucleotides between read pairs. If the target in such experiments is sequenced at a level to provide redundant coverage, it may be possible to bridge these gaps using bioinformatics methods. Konnector is a local de novo assembly tool that addresses this problem. Here we report on version 2.0 of our tool.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26399504</PMID><DateCompleted><Year>2016</Year><Month>07</Month><Day>13</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1755-8794</ISSN><JournalIssue CitedMedium="Internet"><Volume>8 Suppl 3</Volume><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>BMC medical genomics</Title><ISOAbbreviation>BMC Med Genomics</ISOAbbreviation></Journal><ArticleTitle>Konnector v2.0: pseudo-long reads from paired-end sequencing data.</ArticleTitle><Pagination><MedlinePgn>S1</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1755-8794-8-S3-S1</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Reading the nucleotides from two ends of a DNA fragment is called paired-end tag (PET) sequencing. When the fragment length is longer than the combined read length, there remains a gap of unsequenced nucleotides between read pairs. If the target in such experiments is sequenced at a level to provide redundant coverage, it may be possible to bridge these gaps using bioinformatics methods. Konnector is a local de novo assembly tool that addresses this problem. Here we report on version 2.0 of our tool.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Konnector uses a probabilistic and memory-efficient data structure called Bloom filter to represent a k-mer spectrum - all possible sequences of length k in an input file, such as the collection of reads in a PET sequencing experiment. It performs look-ups to this data structure to construct an implicit de Bruijn graph, which describes (k-1) base pair overlaps between adjacent k-mers. It traverses this graph to bridge the gap between a given pair of flanking sequences.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Here we report the performance of Konnector v2.0 on simulated and experimental datasets, and compare it against other tools with similar functionality. We note that, representing k-mers with 1.5 bytes of memory on average, Konnector can scale to very large genomes. With our parallel implementation, it can also process over a billion bases on commodity hardware.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vandervalk</LastName><ForeName>Benjamin P</ForeName><Initials>BP</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Chen</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Xue</LastName><ForeName>Zhuyi</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Raghavan</LastName><ForeName>Karthika</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Chu</LastName><ForeName>Justin</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Mohamadi</LastName><ForeName>Hamid</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Jackman</LastName><ForeName>Shaun D</ForeName><Initials>SD</Initials></Author><Author ValidYN="Y"><LastName>Chiu</LastName><ForeName>Readman</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Warren</LastName><ForeName>René L</ForeName><Initials>RL</Initials></Author><Author ValidYN="Y"><LastName>Birol</LastName><ForeName>Inanç</ForeName><Initials>I</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 HG007182</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01HG007182</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>09</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Med Genomics</MedlineTA><NlmUniqueID>101319628</NlmUniqueID><ISSNLinking>1755-8794</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>9</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>9</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>7</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26399504</ArticleId><ArticleId IdType="pii">1755-8794-8-S3-S1</ArticleId><ArticleId IdType="doi">10.1186/1755-8794-8-S3-S1</ArticleId><ArticleId IdType="pmc">PMC4582294</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Bioinformatics. 2013 Jul 1;29(13):1679-81</Citation><ArticleIdList><ArticleId IdType="pubmed">23620362</ArticleId></ArticleIdList></Reference><Reference><Citation>Gigascience. 2012 Dec 27;1(1):18</Citation><ArticleIdList><ArticleId IdType="pubmed">23587118</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2013 Jun 1;29(11):1455-7</Citation><ArticleIdList><ArticleId IdType="pubmed">23603334</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2008 Feb;18(2):324-30</Citation><ArticleIdList><ArticleId IdType="pubmed">18083777</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2008 Dec 15;24(24):2818-24</Citation><ArticleIdList><ArticleId IdType="pubmed">18952627</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Jun 1;28(11):1533-5</Citation><ArticleIdList><ArticleId IdType="pubmed">22508794</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2013 Nov 1;29(21):2669-77</Citation><ArticleIdList><ArticleId IdType="pubmed">23990416</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2012;13 Suppl 14:S8</Citation><ArticleIdList><ArticleId IdType="pubmed">23095524</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Sep 1;25(17):2283-5</Citation><ArticleIdList><ArticleId IdType="pubmed">19542151</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2012 Mar;22(3):549-56</Citation><ArticleIdList><ArticleId IdType="pubmed">22156294</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2000 Mar 24;287(5461):2196-204</Citation><ArticleIdList><ArticleId IdType="pubmed">10731133</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2009 Jun;19(6):1117-23</Citation><ArticleIdList><ArticleId IdType="pubmed">19251739</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2010 Mar 15;26(6):841-2</Citation><ArticleIdList><ArticleId IdType="pubmed">20110278</ArticleId></ArticleIdList></Reference><Reference><Citation>Algorithms Mol Biol. 2013 Sep 16;8(1):22</Citation><ArticleIdList><ArticleId IdType="pubmed">24040893</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2009;10(3):R25</Citation><ArticleIdList><ArticleId IdType="pubmed">19261174</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9748-53</Citation><ArticleIdList><ArticleId IdType="pubmed">11504945</ArticleId></ArticleIdList></Reference><Reference><Citation>J Comput Biol. 2010 Nov;17(11):1519-33</Citation><ArticleIdList><ArticleId IdType="pubmed">20958248</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Nov 15;28(22):2870-4</Citation><ArticleIdList><ArticleId IdType="pubmed">23044551</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2013 Jun 15;29(12):1492-7</Citation><ArticleIdList><ArticleId IdType="pubmed">23698863</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2013 Apr 15;29(8):1072-5</Citation><ArticleIdList><ArticleId IdType="pubmed">23422339</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2012;13(6):R56</Citation><ArticleIdList><ArticleId IdType="pubmed">22731987</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2010 Jul 1;26(13):1595-600</Citation><ArticleIdList><ArticleId IdType="pubmed">20472541</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Nov 1;27(21):2957-63</Citation><ArticleIdList><ArticleId IdType="pubmed">21903629</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Jul 15;25(14):1754-60</Citation><ArticleIdList><ArticleId IdType="pubmed">19451168</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2015;16:230</Citation><ArticleIdList><ArticleId IdType="pubmed">26209068</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Birol, Inanc" sort="Birol, Inanc" uniqKey="Birol I" first="Inanç" last="Birol">Inanç Birol</name><name sortKey="Chiu, Readman" sort="Chiu, Readman" uniqKey="Chiu R" first="Readman" last="Chiu">Readman Chiu</name><name sortKey="Chu, Justin" sort="Chu, Justin" uniqKey="Chu J" first="Justin" last="Chu">Justin Chu</name><name sortKey="Jackman, Shaun D" sort="Jackman, Shaun D" uniqKey="Jackman S" first="Shaun D" last="Jackman">Shaun D. Jackman</name><name sortKey="Mohamadi, Hamid" sort="Mohamadi, Hamid" uniqKey="Mohamadi H" first="Hamid" last="Mohamadi">Hamid Mohamadi</name><name sortKey="Raghavan, Karthika" sort="Raghavan, Karthika" uniqKey="Raghavan K" first="Karthika" last="Raghavan">Karthika Raghavan</name><name sortKey="Vandervalk, Benjamin P" sort="Vandervalk, Benjamin P" uniqKey="Vandervalk B" first="Benjamin P" last="Vandervalk">Benjamin P. Vandervalk</name><name sortKey="Warren, Rene L" sort="Warren, Rene L" uniqKey="Warren R" first="René L" last="Warren">René L. Warren</name><name sortKey="Xue, Zhuyi" sort="Xue, Zhuyi" uniqKey="Xue Z" first="Zhuyi" last="Xue">Zhuyi Xue</name><name sortKey="Yang, Chen" sort="Yang, Chen" uniqKey="Yang C" first="Chen" last="Yang">Chen Yang</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001494 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 001494 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:26399504
|texte= Konnector v2.0: pseudo-long reads from paired-end sequencing data.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:26399504" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |