data structure

Efficient Construction of Hierarchical Overlap Graphs

The hierarchical overlap graph (HOG for short) is an overlap encoding graph that efficiently represents overlaps from a given set $P$ of $n$ strings. A previously known algorithm constructs the HOG in $O(|| P || + n^2)$ time and $O(|| P || +n times …

Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data

Philippe et al. (2011) proposed a data structure called Gk arrays for indexing and querying large collections of high-throughput sequencing data in main-memory. The data structure supports versatile queries for counting, locating, and analysing the …