Difference between revisions of "IDBA-UD"

Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:BioinformaticsCategory:Metagenomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|idba}} |{{#vardefine:url|http://i.cs.hku.hk/~alse/...")
Line 68: Line 68:
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
* Validated 4/5/2018

Revision as of 17:45, 5 April 2018


idba website  

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.

Required Modules


  • idba

System Variables

  • HPC_{{#uppercase:idba}}_DIR
  • HPC_{{#uppercase:idba}}_BIN


  • Validated 4/5/2018