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 …

There is growing interest in using genetic variants to augment the reference genome into a
graph genome, with alternative sequences, to improve read alignment accuracy and reduce …

Motivation Graphs are commonly used to represent sets of sequences. Either edges or
nodes can be labeled by sequences, so that each path in the graph spells a concatenated …

Motivation Constructing high-quality haplotype-resolved de novo assemblies of diploid
genomes is important for revealing the full extent of structural variation and its role in health …

Motivation Antimicrobial resistance (AMR) remains a major threat to global health. Profiling
the collective AMR genes within a metagenome (the 'resistome') facilitates greater …

Background While the reconstruction of transcripts from a sample of RNA-Seq data is a
computationally expensive and complicated task, the detection of splicing events from RNA …

Motivation Viruses populate their hosts as a viral quasispecies: a collection of genetically
related mutant strains. Viral quasispecies assembly is the reconstruction of strain-specific …

With the emergence of low-cost high-throughput sequencing technologies, numerous
studies have shown that a single genome is not enough to identify all the genes present in a …

Motivation Reconstructing high-quality haplotype-resolved assemblies for related
individuals has important applications in Mendelian diseases and population genomics …

Graph-based representations are considered to be the future for reference genomes, as they
allow integrated representation of the steadily increasing data on individual variation …