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Pathset graphs : A novel approach for comprehensive utilization of paired reads in genome assembly. / Pham, Son K.; Antipov, Dmitry; Sirotkin, Alexander; Tesler, Glenn; Pevzner, Pavel A.; Alekseyev, Max A.

Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. 2012. стр. 200-212 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Том 7262 LNBI).

Результаты исследований: Публикации в книгах, отчётах, сборниках, трудах конференций › статья в сборнике материалов конференции › научная › Рецензирование

Harvard

Pham, SK, Antipov, D, Sirotkin, A, Tesler, G, Pevzner, PA & Alekseyev, MA 2012, Pathset graphs: A novel approach for comprehensive utilization of paired reads in genome assembly. в Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Том. 7262 LNBI, стр. 200-212, 16th Annual International Conference on Research in Computational Molecular Biology, Barcelona, Испания, 21/04/12. https://doi.org/10.1007/978-3-642-29627-7_21

APA

Pham, S. K., Antipov, D., Sirotkin, A., Tesler, G., Pevzner, P. A., & Alekseyev, M. A. (2012). Pathset graphs: A novel approach for comprehensive utilization of paired reads in genome assembly. в Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings (стр. 200-212). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Том 7262 LNBI). https://doi.org/10.1007/978-3-642-29627-7_21

Vancouver

Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA. Pathset graphs: A novel approach for comprehensive utilization of paired reads in genome assembly. в Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. 2012. стр. 200-212. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-29627-7_21

Author

Pham, Son K. ; Antipov, Dmitry ; Sirotkin, Alexander ; Tesler, Glenn ; Pevzner, Pavel A. ; Alekseyev, Max A. / Pathset graphs : A novel approach for comprehensive utilization of paired reads in genome assembly. Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. 2012. стр. 200-212 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

BibTeX

@inproceedings{b9c58d250afe4b2ca3c6e9f82021141a,
title = "Pathset graphs: A novel approach for comprehensive utilization of paired reads in genome assembly",
abstract = "One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.",
author = "Pham, {Son K.} and Dmitry Antipov and Alexander Sirotkin and Glenn Tesler and Pevzner, {Pavel A.} and Alekseyev, {Max A.}",
year = "2012",
doi = "10.1007/978-3-642-29627-7_21",
language = "English",
isbn = "9783642296260",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
pages = "200--212",
booktitle = "Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings",
note = "16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012 ; Conference date: 21-04-2012 Through 24-04-2012",

}

RIS

TY - GEN

T1 - Pathset graphs

T2 - 16th Annual International Conference on Research in Computational Molecular Biology

AU - Pham, Son K.

AU - Antipov, Dmitry

AU - Sirotkin, Alexander

AU - Tesler, Glenn

AU - Pevzner, Pavel A.

AU - Alekseyev, Max A.

PY - 2012

Y1 - 2012

N2 - One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

AB - One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

UR - http://www.scopus.com/inward/record.url?scp=84860808270&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-29627-7_21

DO - 10.1007/978-3-642-29627-7_21

M3 - Conference contribution

AN - SCOPUS:84860808270

SN - 9783642296260

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 200

EP - 212

BT - Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings

Y2 - 21 April 2012 through 24 April 2012

ER -

ID: 100630943