title: KGBassembler: a karyotype-based genome assembler for Brassicaceae species.
abstract: BACKGROUND
  The Brassicaceae family includes the most important plant model Arabidopsis thaliana and many cruciferous vegetable crops. A number of close relatives of Arabidopsis and economically important Brassica species are being sequenced with whole-genome shotgun sequencing technologies. However, de novo assembly of full chromosomes is difficult, since many non-model Brassicaceae species are lacking genetic and/or physical maps. As a unique feature for Brassicaceae, the genome of each member is composed of 24 conserved chromosomal blocks, and the arrangement of the 24 blocks can be obtained from karyotype analysis via comparative chromosome painting experiments. Taking this advantage, we developed a bioinformatic tool named KGBassembler to automatically finalize assembly of full chromosomes from contigs and/or scaffolds based on available karyotypes of Brassicaceae species.
  
  
  BACKGROUND
  KGBassembler was implemented in C++ with a graphical user interface. It is freely available to academic users at http://www.cmbb.arizona.edu/KGBassembler/.
  
  
  BACKGROUND
  xwang1@cals.arizona.edu.
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Chuang
authors.initials: C
authors.lastname: Ma
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.forename: Mingming
authors.initials: M
authors.lastname: Xin
authors.forename: Ruolin
authors.initials: R
authors.lastname: Yang
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D019607:Brassicaceae / Q000235:genetics*; D020223:Chromosome Painting; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D020451:Contig Mapping; D018745:Genome, Plant; D007621:Karyotyping; D016415:Sequence Alignment; D014584:User-Computer Interface