Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …

Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …

Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although
each path in the graph is a potential haplotype, most paths are non-biological, unlikely …

Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-
genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with …

Availability of extensive genetic data across multiple individuals and populations is driving
the growing importance of graph-based reference representations. Aligning sequences to …

Exact string matching in labeled graphs is the problem of searching paths of a graph G=(V,
E) such that the concatenation of their node labels is equal to the given pattern string P [1 …

An index for a finite automaton is a powerful data structure that supports locating paths
labeled with a query pattern, thus solving pattern matching on the underlying regular …

The κ-spectrum of a string is the set of all distinct substrings of length κ occurring in the
string. This is a lossy but computationally convenient representation of the information in the …

The string matching problem on a node-labeled graph G=(V, E) asks whether a given
pattern string P equals the concatenation of node labels of some path in G. This is a basic …

For the first time we provide a succinct pattern matching index for arbitrary graphs that can
be built in polynomial time, while improving both space and query time bounds from SODA …