Using a priori knowledge to align sequencing reads to their exact genomic position

  • The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman–Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (∼92%).

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Metadaten
Author:René BöttcherORCiD, Ronny Amberg, F. P. Ruzius, V. Guryev, Wim F. J. Verhaegh, Peter Beyerlein, P. J. van der Zaag
URN:urn:nbn:de:kobv:526-opus4-6407
DOI:https://doi.org/10.1093/nar/gks393
ISSN:1362-4962
Parent Title (English):Nucleic Acids Research
Document Type:Article
Language:English
Year of Publication:2012
Publishing Institution:Technische Hochschule Wildau
Release Date:2016/07/06
Volume:40
Issue:16
Pagenumber:11
Source:René Böttcher, Ronny Amberg, F. P. Ruzius, V. Guryev, Wim F. J. Verhaegh, Peter Beyerlein, and P. J. van der Zaag Using a priori knowledge to align sequencing reads to their exact genomic position Nucl. Acids Res. (2012) 40 (16): e125 first published online May 11, 2012 doi:10.1093/nar/gks393
Institutes:Fachbereich Ingenieurwesen / Wirtschaftsingenieurwesen (bis 8/2014)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (German):Creative Commons - CC BY-NC 3.0 - Namensnennung-Nicht kommerziell 3.0 Unported