Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
Dutilh BE, Huynen MA, Strous M (2009)
BIOINFORMATICS 25(21): 2878-2881.
Zeitschriftenaufsatz
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Autor*in
Dutilh, Bas E.;
Huynen, Martijn A.;
Strous, MarcUniBi
Einrichtung
Abstract / Bemerkung
Motivation: Most microbial species can not be cultured in the laboratory. Metagenomic sequencing may still yield a complete genome if the sequenced community is enriched and the sequencing coverage is high. However, the complexity in a natural population may cause the enrichment culture to contain multiple related strains. This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold. Results: Here, we map short metagenomic sequencing reads from a population of strains to a related reference genome, and compose a genome that captures the consensus of the population's sequences. We show that by iteration of the mapping and assembly procedure, the coverage increases while the similarity with the reference genome decreases. This indicates that the assembly becomes less dependent on the reference genome and approaches the consensus genome of the multi-strain population.
Erscheinungsjahr
2009
Zeitschriftentitel
BIOINFORMATICS
Band
25
Ausgabe
21
Seite(n)
2878-2881
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1590210
Zitieren
Dutilh BE, Huynen MA, Strous M. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. BIOINFORMATICS. 2009;25(21):2878-2881.
Dutilh, B. E., Huynen, M. A., & Strous, M. (2009). Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. BIOINFORMATICS, 25(21), 2878-2881. https://doi.org/10.1093/bioinformatics/btp377
Dutilh, Bas E., Huynen, Martijn A., and Strous, Marc. 2009. “Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly”. BIOINFORMATICS 25 (21): 2878-2881.
Dutilh, B. E., Huynen, M. A., and Strous, M. (2009). Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. BIOINFORMATICS 25, 2878-2881.
Dutilh, B.E., Huynen, M.A., & Strous, M., 2009. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. BIOINFORMATICS, 25(21), p 2878-2881.
B.E. Dutilh, M.A. Huynen, and M. Strous, “Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly”, BIOINFORMATICS, vol. 25, 2009, pp. 2878-2881.
Dutilh, B.E., Huynen, M.A., Strous, M.: Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. BIOINFORMATICS. 25, 2878-2881 (2009).
Dutilh, Bas E., Huynen, Martijn A., and Strous, Marc. “Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly”. BIOINFORMATICS 25.21 (2009): 2878-2881.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
22 Zitationen in Europe PMC
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Pelletier E, Kreimeyer A, Bocs S, Rouy Z, Gyapay G, Chouari R, Riviere D, Ganesan A, Daegelen P, Sghir A, Cohen GN, Medigue C, Weissenbach J, Le Paslier D., J. Bacteriol. 190(7), 2008
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PMID: 18245282
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Salzberg SL, Sommer DD, Puiu D, Lee VT., PLoS Comput. Biol. 4(9), 2008
PMID: 18818729
Salzberg SL, Sommer DD, Puiu D, Lee VT., PLoS Comput. Biol. 4(9), 2008
PMID: 18818729
AUTHOR UNKNOWN, 0
Environmental genome shotgun sequencing of the Sargasso Sea.
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO., Science 304(5667), 2004
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PMID: 15001713
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
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PMID: 10890397
Zhang Z, Schwartz S, Wagner L, Miller W., J. Comput. Biol. 7(1-2), 2000
PMID: 10890397
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