IDBA-UD

 

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. 

 

Documentation

  • IDBA-UD web site
  • Peng, Y., et al. (2010) IDBA- A Practical Iterative de Bruijn Graph De Novo Assembler. RECOMB. Lisbon.
  • Peng, Y., et al. (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, 28, 1420-1428.

 

Usage

  • Bridges

To see what versions of IDBA-UD are available type

module avail idba-ud

To see what other modules are needed, what commands are available and how to get additional help type

module help  idba-ud

To use IDBA-UD, include a command like this in your batch script to load the IDBA-UD module:

module load idba-ud

Be sure you also load any other modules needed, as listed by the module help idba-ud command.

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