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Bliss: A New Read Overlap Detection Algorithm
Sayali Davalbhakta
Pages - 1 - 7 | Revised - 10-07-2014 | Published - 10-08-2014
MORE INFORMATION
KEYWORDS
Overlap Detection, De Novo Assembly, Overlap-layout-consensus, OLC Assemblers, DNA Sequencing, Whole Genome Shotgun Assembly.
ABSTRACT
Many assemblers carry out heuristic based overlap detection to avoid string comparisons. But heuristics skips many true overlaps. Also, the order of the number of read pairs compared for overlaps is higher than the order of n. In the raw approach it would be n 2 where every read is compared to every other read. Some assemblers have used a hybrid approach to bring the order down from n 2. Here is an algorithm which works with 100% accuracy. As there is no heuristics involved, it is able to report all the overlaps in a given set of reads without actual string comparisons. It achieves this purely by querying the k-mer position data. Moreover, the number of read pairs compared is proportional to the number of reads present i.e. of the order of n.
| 1 | Davalbhakta, S. K. (2014). Read Overlap Detection in De Novo Assembly (Doctoral dissertation, department of computer engineering and information technology, college of engineering, pune). |
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| Sayali Davalbhakta. “Throwing Away k-mer Strings” Submitted for publication. | |
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Miss Sayali Davalbhakta
Department of Computer Engineering and IT College of Engineering, Pune Shivaji Nagar, 411005, India - India
sayalid@gmail.com
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