title: An efficient approach to BAC based assembly of complex genomes.
abstract: BACKGROUND
  There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success.
  
  
  RESULTS
  We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes.
  
  
  CONCLUSIONS
  We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia ; Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, P. O. Box 30197, Nairobi, 00100 Kenya.
authors.forename: Paul
authors.initials: P
authors.lastname: Visendi
authors.affiliation: CSIRO Plant Industry, Brisbane, QLD 4072 Australia.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Berkman
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia.
authors.forename: Satomi
authors.initials: S
authors.lastname: Hayashi
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia.
authors.forename: Agnieszka A
authors.initials: AA
authors.lastname: Golicz
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia ; School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia.
authors.forename: Philipp E
authors.initials: PE
authors.lastname: Bayer
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia ; School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Ruperao
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia ; School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia.
authors.forename: Bhavna
authors.initials: B
authors.lastname: Hurgobin
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia.
authors.forename: Juan
authors.initials: J
authors.lastname: Montenegro
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia ; School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia.
authors.forename: Chon-Kit Kenneth
authors.initials: CK
authors.lastname: Chan
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic.
authors.forename: Helena
authors.initials: H
authors.lastname: Staňková
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia ; School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic.
authors.forename: Hana
authors.initials: H
authors.lastname: Šimková
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia ; School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia.
authors.forename: David
authors.identifier: 0000-0001-7599-6760
authors.initials: D
authors.lastname: Edwards
keywords: 7DS; Assembly; BAC; Next-generation sequencing; SASSY; Saccharum spp; Triticum aestivum