Laboratory of Computational Biology and Bioinformatics        


KGBassembler (Brassicaceae genome assembler) is a C++ based tool for assembling contigs and/or scaffolds to full chromosomes based on the karyotype maps of Brassicaceae species and without the need of genetic and physical maps.


KGBassembler is featured with a graphical user interface (GUI) for users without the need of programming.

Easy to run

No installation is required to implement KGBassembler. Just download the implementation files from this website and use it directly.

Download KGBassembler

Currently KGBassembler supports Linux and Winodws.

For Windows users:
For Linux users:

Karyotype files:

karyotype of A. thaliana (n=5) (~1 Kb)
karyotype of E. salsugineum (n=7) (~1 Kb)
karyotype of S. parvula (n=7) (~1 Kb)
karyotype of T. parvula (n=7) (~1 Kb)
karyotype of A. lyrata (n=8) (~1 Kb)

Example files:
configure file (~1 Kb)
karyotype file (~1 Kb)
contig sequence file (~130 Mb)
BLAT alignment file (~40 Mb).

User Manual

manual.pdf is provided here.



Chuang Ma, Hao Chen, Mingming Xin, Ruolin Yang and Xiangfeng Wang. KGBassembler: a karyotype-based genome assembler for Brassicaceae species. 2012, 28 (23):3141-3143. doi: 10.1093/bioinformatics/bts586.