Bioinfomatics Research Group

Computer Science, The University of Hong Kong

What Is 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.

Current Release

Latest version is avaliable in GitHub.

IDBA 1.1.1

Some bug fixes. Use 16 bits to store read length. All IDBA assemblers will support read length up to 65535 by modifying kMaxShortSequence in src/sequence/short_sequence.h

Download release

IDBA, IDBA-UD, IDBA-Hybrid and IDBA-Tran all in one package Released Oct 18, 2012

All IDBA (iterative de Bruijn graph assembler) series assemblers are refined and included in this package. Plenty of errors are fixed and scaffolding on multiple levels of paired-end reads are supported in IDBA, IDBA-UD and IDBA-Hybrid.

The basic IDBA is included only for comparison.
If you are assembling genomic data without reference, please use IDBA-UD.
If you are assembling genomic data with a similar reference genome, please use IDBA-Hybrid.
If you are assembling transcriptome data, please use IDBA-Tran.

Download release 1.1.0


IDBA-Tran package Released Sep 5, 2012

Download release

Please follow the instruction in README file to run the software.


The sample of rice transcriptome data used in IDBA-Tran paper can be download here. Please follow the README file in the package to generate the simulated data.

Experiment Parameters

The parameters used in the sample data is as following:

idba_tran -r reads.fa -o out-dir --mink 20 --maxk 50 --step 5


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.


E-mail: Peng Yu

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