Briefings in Bioinformatics Advance Access originally published online on May 29, 2009
Briefings in Bioinformatics 2009 10(4):354-366; doi:10.1093/bib/bbp026
Genome assembly reborn: recent computational challenges
Mihai Pop
Corresponding author. Mihai Pop, Department of Computer Science, Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, Room 3120F, University of Maryland, College Park, MD 20742, USA. E-mail: [email protected]
Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, leading to new computational challenges. In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain.
Keywords: genome assembly, genome sequencing, next generation sequencing technologies
Submitted: March 2, 2009. Received (in revised form): April 18, 2009.
Briefings in Bioinformatics 2009 10(4):354-366; doi:10.1093/bib/bbp026
Genome assembly reborn: recent computational challenges
Mihai Pop
Corresponding author. Mihai Pop, Department of Computer Science, Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, Room 3120F, University of Maryland, College Park, MD 20742, USA. E-mail: [email protected]
Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, leading to new computational challenges. In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain.
Keywords: genome assembly, genome sequencing, next generation sequencing technologies
Submitted: March 2, 2009. Received (in revised form): April 18, 2009.