title: Physical map-assisted whole-genome shotgun sequence assemblies.
abstract: We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical maps. Clone sizes and overlaps derived from clone fingerprints are used for the calculation of length constraints between any two BAC neighbors sharing 40% of their size. These constraints are used to promote the linkage and guide the arrangement of sequence contigs within a sequence scaffold at the layout phase of WGS assemblies. This process is facilitated by FASSI, a stand-alone application that calculates BAC end and BAC overlap length constraints from clone fingerprint map contigs created by the FPC package. FASSI is designed to work with the assembly tool PCAP, but its output can be formatted to work with other WGS assembly algorithms able to use length constraints for individual clones. The FASSI method is simple to implement, potentially cost-effective, and has resulted in the increase of scaffold contiguity for both the Drosophila melanogaster and Cryptococcus gattii genomes when compared to a control assembly without map-derived constraints. A 6.5-fold coverage draft DNA sequence of the Pan troglodytes (chimpanzee) genome was assembled using map-derived constraints and resulted in a 26.1% increase in scaffold contiguity.
authors.affiliation: British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.
authors.forename: René L
authors.initials: RL
authors.lastname: Warren
authors.forename: Dmitry
authors.initials: D
authors.lastname: Varabei
authors.forename: Darren
authors.initials: D
authors.lastname: Platt
authors.forename: Xiaoqiu
authors.initials: X
authors.lastname: Huang
authors.forename: David
authors.initials: D
authors.lastname: Messina
authors.forename: Shiaw-Pyng
authors.initials: SP
authors.lastname: Yang
authors.forename: James W
authors.initials: JW
authors.lastname: Kronstad
authors.forename: Martin
authors.initials: M
authors.lastname: Krzywinski
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.forename: John W
authors.initials: JW
authors.lastname: Wallis
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.forename: Asif T
authors.initials: AT
authors.lastname: Chinwalla
authors.forename: Jacqueline E
authors.initials: JE
authors.lastname: Schein
authors.forename: Asim S
authors.initials: AS
authors.lastname: Siddiqui
authors.forename: Marco A
authors.initials: MA
authors.lastname: Marra
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D003454:Cryptococcus / Q000235:genetics*; D030561:Databases, Nucleic Acid; D004331:Drosophila melanogaster / Q000235:genetics*; D016678:Genome; D002679:Pan troglodytes / Q000235:genetics*; D020161:Physical Chromosome Mapping; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software