High-throughput sequencing data sets are usually deposited in public repositories (eg, the
European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached …

Various graphs such as web or social networks may contain up to trillions of edges.
Compressing such datasets can accelerate graph processing by reducing the amount of I/O …

The recent advances in sequencing technologies enable the assembly of individual
genomes to the quality of the reference genome. How to integrate multiple genomes from …

Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based
assemblers reduce the complexity by compacting paths into single vertices, but this is …

Compacted de Bruijn graphs are one of the most fundamental data structures in
computational genomics. Colored compacted de Bruijn graphs are a variant built on a …

Sequence-level searches on large collections of RNA sequencing experiments, such as the
NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the …

We present COBS, a COmpact Bit-sliced Signature index, which is a cross-over between an
inverted index and Bloom filters. Our target application is to index k-mers of DNA samples or …

The amount of biological sequencing data available in public repositories is growing
exponentially, forming an invaluable biomedical research resource. Yet, making all this …

Motivation Indexing reference sequences for search—both individual genomes and
collections of genomes—is an important building block for many sequence analysis tasks …

The analysis of biological sequencing data has been one of the biggest applications of
string algorithms. The approaches used in many such applications are based on the …