Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps
Identifieur interne : 000591 ( Ncbi/Merge ); précédent : 000590; suivant : 000592Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps
Auteurs : Michael Roberts [États-Unis] ; Aleksey V. Zimin [États-Unis] ; Wayne Hayes [États-Unis] ; Brian R. Hunt [États-Unis] ; Cevat Ustun [États-Unis] ; James R. White [États-Unis] ; Paul Havlak [États-Unis] ; James Yorke [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Rats.
- Animaux, Chromosomes artificiels de bactérie, Génome, Reproductibilité des résultats.
English descriptors
- KwdEn :
- MESH :
- genetics : Rats.
- Animals, Chromosomes, Artificial, Bacterial, Genome, Reproducibility of Results.
Abstract
The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version
Url:
DOI: 10.1371/journal.pone.0001836
PubMed: 18350171
PubMed Central: 2266800
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 001058
- to stream Pmc, to step Curation: 001058
- to stream Pmc, to step Checkpoint: 001397
- to stream PubMed, to step Corpus: 002117
- to stream PubMed, to step Curation: 002117
- to stream PubMed, to step Checkpoint: 001F83
Links to Exploration step
PMC:2266800Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps</title>
<author><name sortKey="Roberts, Michael" sort="Roberts, Michael" uniqKey="Roberts M" first="Michael" last="Roberts">Michael Roberts</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Zimin, Aleksey V" sort="Zimin, Aleksey V" uniqKey="Zimin A" first="Aleksey V." last="Zimin">Aleksey V. Zimin</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hayes, Wayne" sort="Hayes, Wayne" uniqKey="Hayes W" first="Wayne" last="Hayes">Wayne Hayes</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R." last="Hunt">Brian R. Hunt</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Ustun, Cevat" sort="Ustun, Cevat" uniqKey="Ustun C" first="Cevat" last="Ustun">Cevat Ustun</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="White, James R" sort="White, James R" uniqKey="White J" first="James R." last="White">James R. White</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Havlak, Paul" sort="Havlak, Paul" uniqKey="Havlak P" first="Paul" last="Havlak">Paul Havlak</name>
<affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yorke, James" sort="Yorke, James" uniqKey="Yorke J" first="James" last="Yorke">James Yorke</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">18350171</idno>
<idno type="pmc">2266800</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266800</idno>
<idno type="RBID">PMC:2266800</idno>
<idno type="doi">10.1371/journal.pone.0001836</idno>
<date when="2008">2008</date>
<idno type="wicri:Area/Pmc/Corpus">001058</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001058</idno>
<idno type="wicri:Area/Pmc/Curation">001058</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001058</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001397</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001397</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed:18350171</idno>
<idno type="wicri:Area/PubMed/Corpus">002117</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002117</idno>
<idno type="wicri:Area/PubMed/Curation">002117</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002117</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001F83</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F83</idno>
<idno type="wicri:Area/Ncbi/Merge">000591</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps</title>
<author><name sortKey="Roberts, Michael" sort="Roberts, Michael" uniqKey="Roberts M" first="Michael" last="Roberts">Michael Roberts</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Zimin, Aleksey V" sort="Zimin, Aleksey V" uniqKey="Zimin A" first="Aleksey V." last="Zimin">Aleksey V. Zimin</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hayes, Wayne" sort="Hayes, Wayne" uniqKey="Hayes W" first="Wayne" last="Hayes">Wayne Hayes</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R." last="Hunt">Brian R. Hunt</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Ustun, Cevat" sort="Ustun, Cevat" uniqKey="Ustun C" first="Cevat" last="Ustun">Cevat Ustun</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="White, James R" sort="White, James R" uniqKey="White J" first="James R." last="White">James R. White</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Havlak, Paul" sort="Havlak, Paul" uniqKey="Havlak P" first="Paul" last="Havlak">Paul Havlak</name>
<affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yorke, James" sort="Yorke, James" uniqKey="Yorke J" first="James" last="Yorke">James Yorke</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
</analytic>
<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2008">2008</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Chromosomes, Artificial, Bacterial</term>
<term>Genome</term>
<term>Rats (genetics)</term>
<term>Reproducibility of Results</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term>
<term>Chromosomes artificiels de bactérie</term>
<term>Génome</term>
<term>Rats (génétique)</term>
<term>Reproductibilité des résultats</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Rats</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Rats</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Chromosomes, Artificial, Bacterial</term>
<term>Genome</term>
<term>Reproducibility of Results</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Chromosomes artificiels de bactérie</term>
<term>Génome</term>
<term>Reproductibilité des résultats</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version <italic>PhrapUMD</italic>
. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the <italic>Rattus norvegicus</italic>
genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at <ext-link ext-link-type="uri" xlink:href="http://www.genome.umd.edu">http://www.genome.umd.edu</ext-link>
. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ewing, B" uniqKey="Ewing B">B Ewing</name>
</author>
<author><name sortKey="Hillier, L" uniqKey="Hillier L">L Hillier</name>
</author>
<author><name sortKey="Wendl, Mc" uniqKey="Wendl M">MC Wendl</name>
</author>
<author><name sortKey="Green, P" uniqKey="Green P">P Green</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ewing, B" uniqKey="Ewing B">B Ewing</name>
</author>
<author><name sortKey="Green, P" uniqKey="Green P">P Green</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sutton, Gg" uniqKey="Sutton G">GG Sutton</name>
</author>
<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
<author><name sortKey="Adams, Md" uniqKey="Adams M">MD Adams</name>
</author>
<author><name sortKey="Kerlavage, Ar" uniqKey="Kerlavage A">AR Kerlavage</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name>
</author>
<author><name sortKey="Sutton, Gg" uniqKey="Sutton G">GG Sutton</name>
</author>
<author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Dew, Im" uniqKey="Dew I">IM Dew</name>
</author>
<author><name sortKey="Fasulo, Dp" uniqKey="Fasulo D">DP Fasulo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Havlak, P" uniqKey="Havlak P">P Havlak</name>
</author>
<author><name sortKey="Chen, R" uniqKey="Chen R">R Chen</name>
</author>
<author><name sortKey="Durbin, Kj" uniqKey="Durbin K">KJ Durbin</name>
</author>
<author><name sortKey="Egan, A" uniqKey="Egan A">A Egan</name>
</author>
<author><name sortKey="Ren, Y" uniqKey="Ren Y">Y Ren</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
<author><name sortKey="Jaffe, Db" uniqKey="Jaffe D">DB Jaffe</name>
</author>
<author><name sortKey="Stanley, K" uniqKey="Stanley K">K Stanley</name>
</author>
<author><name sortKey="Butler, J" uniqKey="Butler J">J Butler</name>
</author>
<author><name sortKey="Gnerre, S" uniqKey="Gnerre S">S Gnerre</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mullikin, Jc" uniqKey="Mullikin J">JC Mullikin</name>
</author>
<author><name sortKey="Ning, Z" uniqKey="Ning Z">Z Ning</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Aparicio, S" uniqKey="Aparicio S">S Aparicio</name>
</author>
<author><name sortKey="Chapman, J" uniqKey="Chapman J">J Chapman</name>
</author>
<author><name sortKey="Stupka, E" uniqKey="Stupka E">E Stupka</name>
</author>
<author><name sortKey="Putnam, N" uniqKey="Putnam N">N Putnam</name>
</author>
<author><name sortKey="Chia, Jm" uniqKey="Chia J">JM Chia</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huang, X" uniqKey="Huang X">X Huang</name>
</author>
<author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name>
</author>
<author><name sortKey="Aluru, S" uniqKey="Aluru S">S Aluru</name>
</author>
<author><name sortKey="Yang, Sp" uniqKey="Yang S">SP Yang</name>
</author>
<author><name sortKey="Hillier, L" uniqKey="Hillier L">L Hillier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Green, P" uniqKey="Green P">P Green</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roberts, M" uniqKey="Roberts M">M Roberts</name>
</author>
<author><name sortKey="Hunt, Br" uniqKey="Hunt B">BR Hunt</name>
</author>
<author><name sortKey="Yorke, Ja" uniqKey="Yorke J">JA Yorke</name>
</author>
<author><name sortKey="Bolanos, R" uniqKey="Bolanos R">R Bolanos</name>
</author>
<author><name sortKey="Delcher, A" uniqKey="Delcher A">A Delcher</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
<author><name sortKey="Yorke, J" uniqKey="Yorke J">J Yorke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schwartz, S" uniqKey="Schwartz S">S Schwartz</name>
</author>
<author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name>
</author>
<author><name sortKey="Smit, A" uniqKey="Smit A">A Smit</name>
</author>
<author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name>
</author>
<author><name sortKey="Baertsch, R" uniqKey="Baertsch R">R Baertsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Kasif, S" uniqKey="Kasif S">S Kasif</name>
</author>
<author><name sortKey="Fleischmann, Rd" uniqKey="Fleischmann R">RD Fleischmann</name>
</author>
<author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name>
</author>
<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<double pmid="18350171"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps</title>
<author><name sortKey="Roberts, Michael" sort="Roberts, Michael" uniqKey="Roberts M" first="Michael" last="Roberts">Michael Roberts</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Zimin, Aleksey V" sort="Zimin, Aleksey V" uniqKey="Zimin A" first="Aleksey V." last="Zimin">Aleksey V. Zimin</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hayes, Wayne" sort="Hayes, Wayne" uniqKey="Hayes W" first="Wayne" last="Hayes">Wayne Hayes</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R." last="Hunt">Brian R. Hunt</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Ustun, Cevat" sort="Ustun, Cevat" uniqKey="Ustun C" first="Cevat" last="Ustun">Cevat Ustun</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="White, James R" sort="White, James R" uniqKey="White J" first="James R." last="White">James R. White</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Havlak, Paul" sort="Havlak, Paul" uniqKey="Havlak P" first="Paul" last="Havlak">Paul Havlak</name>
<affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yorke, James" sort="Yorke, James" uniqKey="Yorke J" first="James" last="Yorke">James Yorke</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">18350171</idno>
<idno type="pmc">2266800</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266800</idno>
<idno type="RBID">PMC:2266800</idno>
<idno type="doi">10.1371/journal.pone.0001836</idno>
<date when="2008">2008</date>
<idno type="wicri:Area/Pmc/Corpus">001058</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001058</idno>
<idno type="wicri:Area/Pmc/Curation">001058</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001058</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001397</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001397</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps</title>
<author><name sortKey="Roberts, Michael" sort="Roberts, Michael" uniqKey="Roberts M" first="Michael" last="Roberts">Michael Roberts</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Zimin, Aleksey V" sort="Zimin, Aleksey V" uniqKey="Zimin A" first="Aleksey V." last="Zimin">Aleksey V. Zimin</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hayes, Wayne" sort="Hayes, Wayne" uniqKey="Hayes W" first="Wayne" last="Hayes">Wayne Hayes</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R." last="Hunt">Brian R. Hunt</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Ustun, Cevat" sort="Ustun, Cevat" uniqKey="Ustun C" first="Cevat" last="Ustun">Cevat Ustun</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="White, James R" sort="White, James R" uniqKey="White J" first="James R." last="White">James R. White</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Havlak, Paul" sort="Havlak, Paul" uniqKey="Havlak P" first="Paul" last="Havlak">Paul Havlak</name>
<affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yorke, James" sort="Yorke, James" uniqKey="Yorke J" first="James" last="Yorke">James Yorke</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America</addr-line>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
</analytic>
<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2008">2008</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version <italic>PhrapUMD</italic>
. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the <italic>Rattus norvegicus</italic>
genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at <ext-link ext-link-type="uri" xlink:href="http://www.genome.umd.edu">http://www.genome.umd.edu</ext-link>
. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ewing, B" uniqKey="Ewing B">B Ewing</name>
</author>
<author><name sortKey="Hillier, L" uniqKey="Hillier L">L Hillier</name>
</author>
<author><name sortKey="Wendl, Mc" uniqKey="Wendl M">MC Wendl</name>
</author>
<author><name sortKey="Green, P" uniqKey="Green P">P Green</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ewing, B" uniqKey="Ewing B">B Ewing</name>
</author>
<author><name sortKey="Green, P" uniqKey="Green P">P Green</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sutton, Gg" uniqKey="Sutton G">GG Sutton</name>
</author>
<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
<author><name sortKey="Adams, Md" uniqKey="Adams M">MD Adams</name>
</author>
<author><name sortKey="Kerlavage, Ar" uniqKey="Kerlavage A">AR Kerlavage</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name>
</author>
<author><name sortKey="Sutton, Gg" uniqKey="Sutton G">GG Sutton</name>
</author>
<author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Dew, Im" uniqKey="Dew I">IM Dew</name>
</author>
<author><name sortKey="Fasulo, Dp" uniqKey="Fasulo D">DP Fasulo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Havlak, P" uniqKey="Havlak P">P Havlak</name>
</author>
<author><name sortKey="Chen, R" uniqKey="Chen R">R Chen</name>
</author>
<author><name sortKey="Durbin, Kj" uniqKey="Durbin K">KJ Durbin</name>
</author>
<author><name sortKey="Egan, A" uniqKey="Egan A">A Egan</name>
</author>
<author><name sortKey="Ren, Y" uniqKey="Ren Y">Y Ren</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
<author><name sortKey="Jaffe, Db" uniqKey="Jaffe D">DB Jaffe</name>
</author>
<author><name sortKey="Stanley, K" uniqKey="Stanley K">K Stanley</name>
</author>
<author><name sortKey="Butler, J" uniqKey="Butler J">J Butler</name>
</author>
<author><name sortKey="Gnerre, S" uniqKey="Gnerre S">S Gnerre</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mullikin, Jc" uniqKey="Mullikin J">JC Mullikin</name>
</author>
<author><name sortKey="Ning, Z" uniqKey="Ning Z">Z Ning</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Aparicio, S" uniqKey="Aparicio S">S Aparicio</name>
</author>
<author><name sortKey="Chapman, J" uniqKey="Chapman J">J Chapman</name>
</author>
<author><name sortKey="Stupka, E" uniqKey="Stupka E">E Stupka</name>
</author>
<author><name sortKey="Putnam, N" uniqKey="Putnam N">N Putnam</name>
</author>
<author><name sortKey="Chia, Jm" uniqKey="Chia J">JM Chia</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huang, X" uniqKey="Huang X">X Huang</name>
</author>
<author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name>
</author>
<author><name sortKey="Aluru, S" uniqKey="Aluru S">S Aluru</name>
</author>
<author><name sortKey="Yang, Sp" uniqKey="Yang S">SP Yang</name>
</author>
<author><name sortKey="Hillier, L" uniqKey="Hillier L">L Hillier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Green, P" uniqKey="Green P">P Green</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roberts, M" uniqKey="Roberts M">M Roberts</name>
</author>
<author><name sortKey="Hunt, Br" uniqKey="Hunt B">BR Hunt</name>
</author>
<author><name sortKey="Yorke, Ja" uniqKey="Yorke J">JA Yorke</name>
</author>
<author><name sortKey="Bolanos, R" uniqKey="Bolanos R">R Bolanos</name>
</author>
<author><name sortKey="Delcher, A" uniqKey="Delcher A">A Delcher</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
<author><name sortKey="Yorke, J" uniqKey="Yorke J">J Yorke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schwartz, S" uniqKey="Schwartz S">S Schwartz</name>
</author>
<author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name>
</author>
<author><name sortKey="Smit, A" uniqKey="Smit A">A Smit</name>
</author>
<author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name>
</author>
<author><name sortKey="Baertsch, R" uniqKey="Baertsch R">R Baertsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Kasif, S" uniqKey="Kasif S">S Kasif</name>
</author>
<author><name sortKey="Fleischmann, Rd" uniqKey="Fleischmann R">RD Fleischmann</name>
</author>
<author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name>
</author>
<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</pmc>
<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Improving Phrap-based assembly of the rat using "reliable" overlaps.</title>
<author><name sortKey="Roberts, Michael" sort="Roberts, Michael" uniqKey="Roberts M" first="Michael" last="Roberts">Michael Roberts</name>
<affiliation wicri:level="4"><nlm:affiliation>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Zimin, Aleksey V" sort="Zimin, Aleksey V" uniqKey="Zimin A" first="Aleksey V" last="Zimin">Aleksey V. Zimin</name>
</author>
<author><name sortKey="Hayes, Wayne" sort="Hayes, Wayne" uniqKey="Hayes W" first="Wayne" last="Hayes">Wayne Hayes</name>
</author>
<author><name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R" last="Hunt">Brian R. Hunt</name>
</author>
<author><name sortKey="Ustun, Cevat" sort="Ustun, Cevat" uniqKey="Ustun C" first="Cevat" last="Ustun">Cevat Ustun</name>
</author>
<author><name sortKey="White, James R" sort="White, James R" uniqKey="White J" first="James R" last="White">James R. White</name>
</author>
<author><name sortKey="Havlak, Paul" sort="Havlak, Paul" uniqKey="Havlak P" first="Paul" last="Havlak">Paul Havlak</name>
</author>
<author><name sortKey="Yorke, James" sort="Yorke, James" uniqKey="Yorke J" first="James" last="Yorke">James Yorke</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2008">2008</date>
<idno type="RBID">pubmed:18350171</idno>
<idno type="pmid">18350171</idno>
<idno type="doi">10.1371/journal.pone.0001836</idno>
<idno type="wicri:Area/PubMed/Corpus">002117</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002117</idno>
<idno type="wicri:Area/PubMed/Curation">002117</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002117</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001F83</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F83</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Improving Phrap-based assembly of the rat using "reliable" overlaps.</title>
<author><name sortKey="Roberts, Michael" sort="Roberts, Michael" uniqKey="Roberts M" first="Michael" last="Roberts">Michael Roberts</name>
<affiliation wicri:level="4"><nlm:affiliation>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Institute for Physical Science and Technology, University of Maryland, College Park, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
<settlement type="city">College Park (Maryland)</settlement>
</placeName>
<orgName type="university">Université du Maryland</orgName>
</affiliation>
</author>
<author><name sortKey="Zimin, Aleksey V" sort="Zimin, Aleksey V" uniqKey="Zimin A" first="Aleksey V" last="Zimin">Aleksey V. Zimin</name>
</author>
<author><name sortKey="Hayes, Wayne" sort="Hayes, Wayne" uniqKey="Hayes W" first="Wayne" last="Hayes">Wayne Hayes</name>
</author>
<author><name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R" last="Hunt">Brian R. Hunt</name>
</author>
<author><name sortKey="Ustun, Cevat" sort="Ustun, Cevat" uniqKey="Ustun C" first="Cevat" last="Ustun">Cevat Ustun</name>
</author>
<author><name sortKey="White, James R" sort="White, James R" uniqKey="White J" first="James R" last="White">James R. White</name>
</author>
<author><name sortKey="Havlak, Paul" sort="Havlak, Paul" uniqKey="Havlak P" first="Paul" last="Havlak">Paul Havlak</name>
</author>
<author><name sortKey="Yorke, James" sort="Yorke, James" uniqKey="Yorke J" first="James" last="Yorke">James Yorke</name>
</author>
</analytic>
<series><title level="j">PloS one</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2008" type="published">2008</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Chromosomes, Artificial, Bacterial</term>
<term>Genome</term>
<term>Rats (genetics)</term>
<term>Reproducibility of Results</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term>
<term>Chromosomes artificiels de bactérie</term>
<term>Génome</term>
<term>Rats (génétique)</term>
<term>Reproductibilité des résultats</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Rats</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Rats</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Chromosomes, Artificial, Bacterial</term>
<term>Genome</term>
<term>Reproducibility of Results</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Chromosomes artificiels de bactérie</term>
<term>Génome</term>
<term>Reproductibilité des résultats</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our "reliable-overlap" algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.</div>
</front>
</TEI>
</pubmed>
</double>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000591 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 000591 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Ncbi |étape= Merge |type= RBID |clé= PMC:2266800 |texte= Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:18350171" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |