Efficient Bubble Enumeration in Directed Graphs
Polymorphisms in DNA- or RNA-seq data lead to recognisable patterns in a de Bruijn graph representation of the reads obtained by sequencing. Such patterns have been called mouths, or bubbles in the literature. They correspond to two vertex-disjoint directed paths between a source s and a target t. Due to the high number of such bubbles that may be present in real data, their enumeration is a major issue concerning the efficiency of dedicated algorithms. We propose in this paper the first linear delay algorithm to enumerate all bubbles with a given source.
KeywordsDirected Graph Alternative Splice Event Next Generation Sequencing Data Linear Delay Target Vertex
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- 2.Sacomoto, G., et al.: KisSplice: de-novo calling alternative splicing events from rna-seq data. In: RECOMB-Seq, BMC Bioinformatics (2012)Google Scholar
- 6.Iqbal, Z., Caccamo, M., Turner, I., Flicek, P., McVean, G.: De novo assembly and genotyping of variants using colored de bruijn graphs. Nature Genetics (2012)Google Scholar
- 8.Pevzner, P.A., Tang, H., Tesler, G.: De novo repeat classification and fragment assembly. In: RECOMB, pp. 213–222 (2004)Google Scholar