Most sequencing data analyses start by aligning sequencing reads to a linear reference
genome, but failure to account for genetic variation leads to reference bias and confounding …

We present pandora, a novel pan-genome graph structure and algorithms for identifying
variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the …

We introduce a compact pangenome representation based on an optimal segmentation
concept that aims to reconstruct founder sequences from a multiple sequence alignment …

Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et
al.(2022)[14] developed the Elastic Founder Graph (EFG) representing an alignment of m …

Motivation Variant calling workflows that utilize a single reference sequence are the de facto
standard elementary genomic analysis routine for resequencing projects. Various ways to …

We study the problem of matching a string in a labeled graph. Previous research has shown
that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem …

We study the problem of matching a string in a labeled graph. Previous research has shown
that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem …

The pattern matching of strings in labeled graphs has been widely studied lately due to its
importance in genomics applications. Unfortunately, even the simplest problem of deciding if …

Indexable elastic founder graphs have been recently proposed as a data structure for
genomics applications supporting fast pattern matching queries. Consider segmenting a …

Most sequencing data analyses start by aligning sequencing reads to a linear reference
genome. But failure to account for genetic variation causes reference bias and confounding …