IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k to perform the assembling task. For all of them, it is very crucial to find a specific value of k. If k is too large, there will be a lot of gap problems in the graph. If k is too small, there will a lot of branch problems. IDBA uses not only one specific k but a range of k values to build the iterative de Bruijn graph. It can keep all the information in graphs with different k values. So, it will perform better than other assemblers.
IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
Bioinformatics Research Group of Hong Kong University
:: MORE INFORMATION
Yu Peng, Henry Leung, S.M. Yiu, Francis Y.L. Chin.
IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler
The 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, 25-28 April 2010.
Bioinformatics. 2012 Jun 1;28(11):1420-8. Epub 2012 Apr 11.
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
Peng Y, Leung HC, Yiu SM, Chin FY.