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.GitHub.
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-Tran package Released Sep 5, 2012
Please follow the instruction in README file to run the software.
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