The efficient algorithm for mapping next generation sequencing reads to reference genome

Patryk Pankiewicz; Wiktor Kuśmirek; Robert M. Nowak

doi:10.1117/12.2536653

6 November 2019 The efficient algorithm for mapping next generation sequencing reads to reference genome

Patryk Pankiewicz, Wiktor Kuśmirek, Robert M. Nowak

Proceedings Volume 11176, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2019; 111761W (2019) https://doi.org/10.1117/12.2536653
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2019, 2019, Wilga, Poland

Abstract

One of the main problem related to genomics is finding similarities between different species represented by DNA sequences. The dynamic programming algorithms (Needleman-Wunsch, Smith-Waterman) give a good measure of similarity, but are not efficient for big data sets. In this study we present the new heuristic algorithm based on common parts of reads. The approach can handle all types of sequencing errors: insertions, deletions and replacements. Our algorithm result is similar to other well known tools. The presented algorithm is implemented in C++, it uses Boost libraries, it internally use threads for parallel computing. This algorithm is a part of the DNA assembler ’dnaasm’. Source code, demo application and supplementary materials are available at project homepage: http://dnaasm.sourceforge.net.

Citation Download Citation

Patryk Pankiewicz, Wiktor Kuśmirek, and Robert M. Nowak "The efficient algorithm for mapping next generation sequencing reads to reference genome", Proc. SPIE 11176, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2019, 111761W (6 November 2019); https://doi.org/10.1117/12.2536653

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available