Linear pattern matching on sparse suffix trees

Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse suffix tree} \cite{KU-96} with appropriately defined suffix links. Assuming, under the standard unit-cost RAM model, that a word can store up to $\log_{\sigma}n$ characters ($\sigma$ the alphabet size), our index takes $O(n/\log_{\sigma}n)$ space, i.e. the same space as the packed string itself. The resulting pattern matching algorithm runs in time $O(m+r^2+r\cdot occ)$, where $m$ is the length of the pattern, $r$ is the actual number of characters stored in a word and $occ$ is the number of pattern occurrences

Scalable String and Suffix Sorting: Algorithms, Techniques, and Tools

This dissertation focuses on two fundamental sorting problems: string sorting and suffix sorting. The first part considers parallel string sorting on shared-memory multi-core machines, the second part external memory suffix sorting using the induced sorting principle, and the third part distributed external memory suffix sorting with a new distributed algorithmic big data framework named Thrill.Comment: 396 pages, dissertation, Karlsruher Instituts f\"ur Technologie (2018). arXiv admin note: text overlap with arXiv:1101.3448 by other author

Indexing arbitrary-length kk-mers in sequencing reads

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments

Lossless fault-tolerant data structures with additive overhead

12th International Symposium, WADS 2011, New York, NY, USA, August 15-17, 2011. ProceedingsWe develop the first dynamic data structures that tolerate δ memory faults, lose no data, and incur only an O(δ ) additive overhead in overall space and time per operation. We obtain such data structures for arrays, linked lists, binary search trees, interval trees, predecessor search, and suffix trees. Like previous data structures, δ must be known in advance, but we show how to restore pristine state in linear time, in parallel with queries, making δ just a bound on the rate of memory faults. Our data structures require Θ(δ) words of safe memory during an operation, which may not be theoretically necessary but seems a practical assumption.Center for Massive Data Algorithmics (MADALGO