Recent rapid development of next generation sequencing (NGS) technologies provided significant impact into genomics field of study enabling implementation of many de novo sequencing projects of new species which was previously confined by technological costs. Along with advancement of NGS there was need for adjustment in assembly programs. New algorithms must cope with massive amounts of data computation in reasonable time limits and processing power and hardware is also an important factor. In this paper, we address the issue of assembly pipeline for de novo genome assembly provided by programs presently available for scientist both as commercial and as open – source software. The implementation of four different approaches – Greedy, Overlap – Layout – Consensus (OLC), De Bruijn and Integrated resulting in variation of performance is the main focus of our discussion with additional insight into issue of short and long reads correction.

Date Published: 25 November 2014
PDF: 8 pages
Proc. SPIE 9290, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2014, 92901X (25 November 2014); doi: 10.1117/12.2075624

Published in SPIE Proceedings Vol. 9290:
Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2014
Ryszard S. Romaniuk, Editor(s)