Abstract
New generation sequencing technologies produce massive data sets of millions of reads, making the compression of sequence read files an important problem. The sequential order of the reads in these files typically conveys no biologically significant information, providing the freedom to reorder them so as to facilitate compression. Similarly, for many problems the orientation of the reads (original or reverse complement) are indistinguishable from an information-theoretic perspective, providing the freedom to optimize the orientation of each read.
In this paper, we introduce a class of algorithmic problems concerned with optimizing read ordering and orientation for sequence compression. We show that most of the interesting variants are hard, but provide heuristics yielding strong approximation guarantees. In particular, we give a linear time 2-approximation algorithm for the optimal ordering/orientation under the prefix match criteria. Further, through experiments on a number of data sets, we demonstrate that this heuristic works well in practice. A prototype implementation of this 2-factor approximation is available at https://github.com/LaoZZZZZ/prefixMatching.
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Acknowledgments
This research was partially supported by NSF Grants DBI-1355990 and IIS-1017181, and a Google Faculty Research Award to Steven Skiena. E. Arkin and J. Mitchell acknowledge support from the National Science Foundation (CCF-1540890) and the US-Israel Binational Science Foundation (BSF project 2010074). Rezaul Chowdhury was supported by NSF grant CCF-1439084. Rob Patro would like to acknowledge Carl Kingsford and Geet Duggal for useful discussions and for helping to initially pose and explore the prefix matching with reversal problem. Finally, we would like to thank the anonymous reviewers for suggestions and comments which greatly improved the manuscript.
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Sichen, Z. et al. (2015). Optimizing Read Reversals for Sequence Compression. 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_14
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DOI: https://doi.org/10.1007/978-3-662-48221-6_14
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