title: Using a priori knowledge to align sequencing reads to their exact genomic position.
abstract: 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%).
authors.affiliation: Philips Research Laboratories, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands.
authors.forename: René
authors.initials: R
authors.lastname: Böttcher
authors.forename: Ronny
authors.initials: R
authors.lastname: Amberg
authors.forename: F P
authors.initials: FP
authors.lastname: Ruzius
authors.forename: V
authors.initials: V
authors.lastname: Guryev
authors.forename: Wim F J
authors.initials: WF
authors.lastname: Verhaegh
authors.forename: Peter
authors.initials: P
authors.lastname: Beyerlein
authors.forename: P J
authors.initials: PJ
authors.lastname: van der Zaag
mesh_terms: D000465:Algorithms; D023281:Genomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA