Abstract
High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high number of sequences sampled from each genome. Such a highly redundant collection of very similar sequences is called a pan-genome. It can be transformed into a set of sequences “colored” by the genomes to which they belong. A colored de-Bruijn graph (C-DBG) extracts from the sequences all colored k-mers, strings of length k, and stores them in vertices. In this paper, we present an alignment-free, reference-free and incremental data structure for storing a pan-genome as a C-DBG: the Bloom Filter Trie. The data structure allows to store and compress a set of colored k-mers, and also to efficiently traverse the graph. Experimental results prove better performance compared to another state-of-the-art data structure.
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Acknowledgments
The authors wish to thank the anonymous reviewers and the authors of SBT for helpful comments. GH and RW are funded by the International DFG Research Training Group GRK 1906/1.
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Holley, G., Wittler, R., Stoye, J. (2015). Bloom Filter Trie – A Data Structure for Pan-Genome Storage. In: Pop, M., Touzet, H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science(), vol 9289. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48221-6_16
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DOI: https://doi.org/10.1007/978-3-662-48221-6_16
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