IDBA
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Application data |
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| Created by | Yu Peng |
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| Biological application domain(s) | Sequence assembly (de novo assembly) |
| Principal bioinformatics method(s) | Sequence assembly |
| Technology | Illumina |
| Created at | Department of Computer Science, The University of Hong Kong |
| Maintained? | Maybe |
| Input format(s) | FASTQ, FASTA |
| Output format(s) | FASTA |
| Operating system(s) | POSIX, Linux, Linux 64 |
Summary: IDBA (Iterative De Bruijn graph short read Assembler) is a short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system
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The de Bruijn graph assembly approach breaks reads into k-mers before assembling them into contigs. The string graph approach forms contigs by connecting two reads with k or more overlapping nucleotides. Both approaches face the problem of false-positive vertices from erroneous reads, missing vertices due to non-uniform coverage and branching due to erroneous reads and repeat regions. A proper choice of k is crucial but for any single k there is always a trade-off: a small k favors the situation of erroneous reads and non-uniform coverage, and a large k favors short repeat regions. We propose an iterative de Bruijn graph approach iterating from small to large k capturing merits of all values in between. With real and simulated data, our IDBA algorithm is superior to all existing algorithms by constructing longer contigs with similar accuracy and using less memory. The running time of IDBA is comparable with existing algorithms.
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