IDBA-Tran

 

IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler for transcriptome. It is purely de novo assembler based on only RNA sequencing reads. IDBA-Tran uses local assembly to reconstructing missing k-mers in low-expressed transcripts and then employs progressive cutoff on contigs to seperate the graph into components. Each component corresponds to one gene in most cases and contains not many transcripts. A heuristic algorithm based on pair-end reads is then used to find the isoforms.

 

Documentation

  • IDBA-TRAN 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-Tran are available type

module avail idba-tran

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

module help  idba-tran

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

module load idba-tran

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

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Send mail to remarks@psc.edu or call the PSC hotline: 412-268-6350.