The Atlas genome assembly system.

TitleThe Atlas genome assembly system.
Publication TypeJournal Article
Year of Publication2004
AuthorsHavlak, P, Chen, R, K Durbin, J, Egan, A, Ren, Y, Song, X-Z, Weinstock, GM, Gibbs, RA
JournalGenome Res
Volume14
Issue4
Pagination721-32
Date Published2004 Apr
ISSN1088-9051
KeywordsAnimals, Chromosomes, Artificial, Bacterial, Contig Mapping, Genome, Rats, Software
Abstract

Atlas is a suite of programs developed for assembly of genomes by a "combined approach" that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford advantages of localized assembly with reduced computational load, and provide a robust method for dealing with repeated sequences. Inclusion of WGS sequences facilitates use of different clone insert sizes and reduces data production costs. A core function of Atlas software is recruitment of WGS sequences into appropriate BACs based on sequence overlaps. Because construction of consensus sequences is from local assembly of these reads, only small (<0.1%) units of the genome are assembled at a time. Once assembled, each BAC is used to derive a genomic layout. This "sequence-based" growth of the genome map has greater precision than with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects.

DOI10.1101/gr.2264004
Alternate JournalGenome Res.
PubMed ID15060016
PubMed Central IDPMC383319
Grant ListU54 HG02345 / HG / NHGRI NIH HHS / United States