Review of general algorithmic features for genome assemblers for next generation sequencers. Academic Article

abstract

• In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.

authors

• Serpedin, Erchin

published proceedings

• Genomics Proteomics Bioinformatics

altmetric score

• 13.7

author list (cited authors)

• Wajid, B., & Serpedin, E.

citation count

• 37

publication date

• April 2012

publisher

• Oxford University Press (OUP)  Publisher

keywords

• Algorithms
• Computational Biology
• Contig Mapping
• Genome
• Sequence Analysis, DNA
• Software

Digital Object Identifier (DOI)

• 10.1016/j.gpb.2012.05.006

start page

• 58

end page

• 73

volume

• 10

issue

• 2

URL

• http://dx.doi.org/10.1016/j.gpb.2012.05.006