Comparative genome assembly - PubMed (original) (raw)
Comparative genome assembly
Mihai Pop et al. Brief Bioinform. 2004 Sep.
Abstract
One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project. With the rapid growth in the number of sequenced genomes has come an increase in the number of organisms for which two or more closely related species have been sequenced. This has created the possibility of building a comparative genome assembly algorithm, which can assemble a newly sequenced genome by mapping it onto a reference genome. We describe here a novel algorithm for comparative genome assembly that can accurately assemble a typical bacterial genome in less than four minutes on a standard desktop computer. The software is available as part of the open-source AMOS project.
Similar articles
- Whole-genome prokaryotic phylogeny.
Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Henz SR, et al. Bioinformatics. 2005 May 15;21(10):2329-35. doi: 10.1093/bioinformatics/bth324. Epub 2004 May 27. Bioinformatics. 2005. PMID: 15166018 - Chaos game representation for comparison of whole genomes.
Joseph J, Sasikumar R. Joseph J, et al. BMC Bioinformatics. 2006 May 5;7:243. doi: 10.1186/1471-2105-7-243. BMC Bioinformatics. 2006. PMID: 16677374 Free PMC article. - Minimus: a fast, lightweight genome assembler.
Sommer DD, Delcher AL, Salzberg SL, Pop M. Sommer DD, et al. BMC Bioinformatics. 2007 Feb 26;8:64. doi: 10.1186/1471-2105-8-64. BMC Bioinformatics. 2007. PMID: 17324286 Free PMC article. - Genome resequencing and genetic variation.
Stratton M. Stratton M. Nat Biotechnol. 2008 Jan;26(1):65-6. doi: 10.1038/nbt0108-65. Nat Biotechnol. 2008. PMID: 18183021 Review. No abstract available. - Homology assessment and molecular sequence alignment.
Phillips AJ. Phillips AJ. J Biomed Inform. 2006 Feb;39(1):18-33. doi: 10.1016/j.jbi.2005.11.005. Epub 2005 Dec 9. J Biomed Inform. 2006. PMID: 16380300 Review.
Cited by
- VirAmp: a galaxy-based viral genome assembly pipeline.
Wan Y, Renner DW, Albert I, Szpara ML. Wan Y, et al. Gigascience. 2015 Apr 28;4:19. doi: 10.1186/s13742-015-0060-y. eCollection 2015. Gigascience. 2015. PMID: 25918639 Free PMC article. - ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.
Tang B, Wang Q, Yang M, Xie F, Zhu Y, Zhuo Y, Wang S, Gao H, Ding X, Zhang L, Zhao G, Zheng H. Tang B, et al. BMC Genomics. 2013 Apr 30;14:289. doi: 10.1186/1471-2164-14-289. BMC Genomics. 2013. PMID: 23627759 Free PMC article. - Personal genome sequencing: current approaches and challenges.
Snyder M, Du J, Gerstein M. Snyder M, et al. Genes Dev. 2010 Mar 1;24(5):423-31. doi: 10.1101/gad.1864110. Genes Dev. 2010. PMID: 20194435 Free PMC article. - A bioinformatician's guide to metagenomics.
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. Kunin V, et al. Microbiol Mol Biol Rev. 2008 Dec;72(4):557-78, Table of Contents. doi: 10.1128/MMBR.00009-08. Microbiol Mol Biol Rev. 2008. PMID: 19052320 Free PMC article. Review. - Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.
Gao S, Sung WK, Nagarajan N. Gao S, et al. J Comput Biol. 2011 Nov;18(11):1681-91. doi: 10.1089/cmb.2011.0170. Epub 2011 Sep 19. J Comput Biol. 2011. PMID: 21929371 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources