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


These file attachments have been under embargo and were made available to the public after the embargo was lifted on 4 June 2012.

Author: Böttcher, R. · Amberg, R. (TFH Wildau) · Ruzius, F.P. (Hubrecht Institute) · Guryev, V. (Hubrecht Institute) · Verhaegh, W.F.J. · Beyerlein, P. · Van der Zaag, P.J.
Embargo lifted:2012-06-04
Publisher: Oxford Journals
Institution: Philips Research
Source:Nucleic Acids Research; authors version
Identifier: MS-32.800
Keywords: dna sequencing, oncology · high throughput dna sequ · molecular digital pathology · sequence alignment · single cell sequencing · single molecule dna sequencing
Rights: (c) Oxford Journals


The use of a priori knowledge in aligning targeted sequencing data is investigated using computational experiments. With conventional aligners such as Bowtie, BWA or MAQ, alignment is performed against the whole genome. Using an alignment method in which the genomic position information from the target capture is incorporated, alignment can be done to just the target region. Investigating the effect of realistic target size, read length, read redundancy, the amount of off-target reads and sequencing error rate, improvements of up to a factor of 8 +/- 0.3 in alignment speed are found using an implementation of the Needleman-Wunsch algorithm which makes use of direct stringcomparison. This results in a total alignment time in target sequencing of around 1 min.

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