What Is IDBA-Hybrid?
IDBA-Hybrid is an iterative De Bruijn Graph De Novo Assembler for hybrid sequencing. It is an extension of IDBA-UD algorithm. It aims at using a closed related reference genome to help de novo assembly, especially when sequencing depth is low. IDBA-Hybrid does alignment between reads and reference first to extract similar regions in the reference genome, and then it correct the similar regions based on the alignment results and apply local assembly technique to resolve potential structure virations. Finally, it groups all the reads and the contigs got from those similar regions to do de novo assembly. The expriments showed it outperforms all existing de novo or hybrid assembly algorithms, especilly when the sequencing depth is low and the reference genome is similar to the target genome.
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
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.
IDBA-Hybrid package Released Sep 5, 2012
Please follow the instruction in README file to run the software.
Data
For chromosome 21 of human and panTro3, please download it form UCSC and use Mason to generate simulated data.
Experiment Parameters
Default parameters are used in all experiments presented in
IDBA-Hybrid paper.
References
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. (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, 28, 1420-1428.
Contact
E-mail: Peng Yu