Improving the Compact Bit-Sliced Signature Index COBS for Large Scale Genomic Data

In this thesis we investigate the potential for improving the Compact Bit-Sliced Signature Index (COBS) [BBGI19] for large scale genomic data. COBS was developed by Bingmann et al. and is an inverted text index based on Bloom filters. It can be used to index k-mers of DNA samples or q-grams of plain text data and is queried using approximate pattern matching based on the k-mer (or q-gram) profile of a query. In their work Bingmann et al. demonstrated a couple of advantages COBS has over other state of the art approximate k-mer-based indices, some of which are extraordinary fast query and construction times, but as well as the fact that COBS can be constructed and queried even if the index does not fit into main memory. This is one of the reasons we decided to look more closely at some areas we could improve COBS. Our main goal is to make COBS more scalable. Scalability is a very important factor when it comes to handling DNA related data. This is because the amount of sequenced data stored in publicly available archives nearly doubles every year, making it difficult to handle even from the perspective of resources alone. We focus on two main areas in which we try to improve COBS. Those are index compression through clustering and distribution. The thesis presents our findings and improvements achieved in respect to those areas

In-Place Parallel Super Scalar Samplesort (IPSSSSo)

We present a sorting algorithm that works in-place, executes in parallel, is cache-efficient, avoids branch-mispredictions, and performs work O(n log n) for arbitrary inputs with high probability. The main algorithmic contributions are new ways to make distribution-based algorithms in-place: On the practical side, by using coarse-grained block-based permutations, and on the theoretical side, we show how to eliminate the recursion stack. Extensive experiments shw that our algorithm IPSSSSo scales well on a variety of multi-core machines. We outperform our closest in-place competitor by a factor of up to 3. Even as a sequential algorithm, we are up to 1.5 times faster than the closest sequential competitor, BlockQuicksort