Abstract
Although hash-based approaches to sequence alignment and genome assembly are long established, their utility is predicated on the rapid identification of exact k-mers from a hash-map or similar data structure. We describe how a fuzzy hash-map can be applied to quickly and accurately align a prokaryotic genome to the reference genome of a related species. Using this technique, a draft genome of Mycoplasma genitalium, sampled at 1X coverage, was accurately anchored against the genome of Mycoplasma pneumoniae. The fuzzy approach to alignment, ordered and orientated more than 65% of the reads from the draft genome in under 10 seconds, with an error rate of <1.5%. Without sacrificing execution speed, fuzzy hash-maps also provide a mechanism for error tolerance and variability in k-mer centric sequence alignment and assembly applications.
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© 2011 Springer-Verlag Berlin Heidelberg
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Healy, J., Chambers, D. (2011). Fast and Accurate Genome Anchoring Using Fuzzy Hash Maps. In: Rocha, M.P., Rodríguez, J.M.C., Fdez-Riverola, F., Valencia, A. (eds) 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Advances in Intelligent and Soft Computing, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19914-1_21
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DOI: https://doi.org/10.1007/978-3-642-19914-1_21
Publisher Name: Springer, Berlin, Heidelberg
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