A new algorithm for genome assembly from short reads

Author

Blazewicz, Jacek ; Bryja, Marcin ; Figlerowicz, Marek ; Gawron, Piotr ; Kasprzak, Marta ; Platt, Darren ; Przybytek, Jakub ; Swiercz, Aleksandra ; Szajkowski, Lukasz

Author_Institution

Inst. of Comput. Sci., Poznan Univ. of Technol., Poznan

fYear

2008

fDate

18-21 May 2008

Firstpage

1

Lastpage

4

Abstract

Progress in bioengineering brought a new approach to DNA sequencing, which aim is to give highly reliable output of low cost and in short time. It is 454 sequencing, based on the pyrosequencing protocol, owned by 454 Life Sciences Corporation. Because of the sequences reliability this method is much better than others for assembly purposes. However, produced sequences are much shorter and there are many more of them, which indicate that the problem is harder. Presented algorithm was created to process data from 454 sequencing method. Usefulness of the algorithm has been proven in tests on raw data generated during sequencing of the whole 1.84 Mbp genome of bacteria Prochlorococcus marinus.

Keywords

DNA; biology computing; genetics; microorganisms; reliability; 454 Life Sciences Corporation; 454 sequencing; DNA sequencing; assembly purposes; bacteria Prochlorococcus marinus; bioengineering; genome assembly; pyrosequencing protocol; sequences reliability; short reads assembly; Assembly; Bioinformatics; Biomedical engineering; Costs; DNA; Genomics; Microorganisms; Protocols; Sequences; Testing;

fLanguage

English

Publisher

ieee

Conference_Titel

Information Technology, 2008. IT 2008. 1st International Conference on

Conference_Location

Gdansk

Print_ISBN

978-1-4244-2244-9

Electronic_ISBN

978-1-4244-2245-6

Type

conf

DOI

10.1109/INFTECH.2008.4621681

Filename

4621681