Bioinfomatics Research Group

Computer Science, The University of Hong Kong

What Is Meta-IDBA?

Meta-IDBA is an iterative De Bruijn Graph De Novo short read assembler specially designed for de novo metagenomic assembly. One of the most difficult problem in metagenomic assembly is that similar subspecies of the same species mix together to make the de Bruijn graph very complicated and intractable. Meta-IDBA handles this problem grouping similar regions of similar subspecies by partitioning the graph into components based on the topological structure of the graph. Each component represents a similar region between subspecies from the same species or even from different species. After the components are separated, all contigs in it are aligned to produced a consensus and also the multiple alignment.

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 current release

(Please note that MetaIDBA is out of maintainance now, we recommend using IDBA-UD instead which generally performs better.)

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 (Meta-IDBA) tool kit 0.19 for 64-bit Linux Released Jan 14,2011

Add Meta-IDBA(Iterative de Bruijn Graph De Novo short read Assembler for Metagenomics based on graph partition) into the toolkit.

Download release

Download class sample 0

Download class sample 1

For more releases download...

Please follow the Installation Guide and User Guide to run the software.


If you use our assembler in your research, please cite our papers.

Peng, Y., et al. (2010) IDBA- A Practical Iterative de Bruijn Graph De Novo Assembler. RECOMB. Lisbon.

Peng, Y., et al. (2011) Meta-IDBA: a de Novo assembler for metagenomic data, Bioinformatics, 27, i94-101.


E-mail: Peng Yu

more support infomation...