KGBassembler

Sep 1, 2012
PubMed

The Brassicaceae family includes the most important plant model Arabidopsis thaliana and many cruciferous vegetable crops. Due to the lack of genetic and/or physical maps for many non-model Brassicaceae species, de novo assembly of full chromosomes is difficult in many experiments designed with short sequencing data. To address this problem, we developed a bioinformatics tool named KGBassembler to automatically finalize assembly of full chromosomes from contigs and/or scaffolds based on available karyotypes of Brassicaceae species (Figure 1). KGBassembler has been successfully applied to the assembly of Eutrema salsugineum, an extremophile model for abiotic stress tolerance studies.

Ma, C., Chen, H., Xin, M., Yang, R., Wang, X. (2012). KGBassembler: a karyotype-based genome assembler for Brassicaceae species Bioinformatics 28(23), 3141-3143. https://dx.doi.org/10.1093/bioinformatics/bts586

algorithms Brassicaceae genetics chromosome painting computational biology methods computer graphics contig mapping genome plant karyotyping sequence alignment user-computer interface
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Chuang Ma
Principal Investigator, Professor, Doctoral Supervisor

My research interests include artificial intelligence, abiotic stress and plant breeding.

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