Abstract
We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers in a DNA sequence of length N has m edges, it can be represented in 4m + o(m) bits. This is much smaller than existing ones. The numbers of outgoing and incoming edges of a node are computed in constant time, and the outgoing and incoming edge with given label are found in constant time and \(\mathcal{O}(k)\) time, respectively. The data structure is constructed in \(\mathcal{O}(Nk \log m/\log\log m)\) time using no additional space.
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Bowe, A., Onodera, T., Sadakane, K., Shibuya, T. (2012). Succinct de Bruijn Graphs. In: Raphael, B., Tang, J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science(), vol 7534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33122-0_18
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DOI: https://doi.org/10.1007/978-3-642-33122-0_18
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