MersV1, Main, Exploration, bibRecord, 002975

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

Identifieur interne : 002975 ( Main/Exploration ); précédent : 002974; suivant : 002976

Improving 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.

RBID : PMC:2266800

Descripteurs français

KwdFr :
- Animaux, Chromosomes artificiels de bactérie, Génome, Rats (génétique), Reproductibilité des résultats.
MESH :
- génétique : Rats.
- Animaux, Chromosomes artificiels de bactérie, Génome, Reproductibilité des résultats.

English descriptors

KwdEn :
- Animals, Chromosomes, Artificial, Bacterial, Genome, Rats (genetics), Reproducibility of Results.
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 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.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266800

DOI: 10.1371/journal.pone.0001836
PubMed: 18350171
PubMed Central: 2266800

Affiliations:

Le document en format XML

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<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>
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<author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name>
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<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Maryland</li>
<li>Texas</li>
</region>
<settlement><li>College Park (Maryland)</li>
</settlement>
<orgName><li>Université du Maryland</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Maryland"><name sortKey="Roberts, Michael" sort="Roberts, Michael" uniqKey="Roberts M" first="Michael" last="Roberts">Michael Roberts</name>
</region>
<name sortKey="Havlak, Paul" sort="Havlak, Paul" uniqKey="Havlak P" first="Paul" last="Havlak">Paul Havlak</name>
<name sortKey="Hayes, Wayne" sort="Hayes, Wayne" uniqKey="Hayes W" first="Wayne" last="Hayes">Wayne Hayes</name>
<name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R." last="Hunt">Brian R. Hunt</name>
<name sortKey="Ustun, Cevat" sort="Ustun, Cevat" uniqKey="Ustun C" first="Cevat" last="Ustun">Cevat Ustun</name>
<name sortKey="White, James R" sort="White, James R" uniqKey="White J" first="James R." last="White">James R. White</name>
<name sortKey="Yorke, James" sort="Yorke, James" uniqKey="Yorke J" first="James" last="Yorke">James Yorke</name>
<name sortKey="Zimin, Aleksey V" sort="Zimin, Aleksey V" uniqKey="Zimin A" first="Aleksey V." last="Zimin">Aleksey V. Zimin</name>
</country>
</tree>
</affiliations>
</record>

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   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     PMC:2266800
   |texte=   Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps
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Serveur d'exploration MERS

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

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