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 …

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 …

The MinHash algorithm has proven effective for rapidly estimating the resemblance of two
genomes or metagenomes. However, this method cannot reliably estimate the containment …

Genome graphs can represent genetic variation and sequence uncertainty. Aligning
sequences to genome graphs is key to many applications, including error correction …

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 …

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 …

Genome-wide association study (GWAS) methods applied to bacterial genomes have
shown promising results for genetic marker discovery or detailed assessment of marker …

The de Bruijn graph is a key data structure in modern computational genomics, and
construction of its compacted variant resides upstream of many genomic analyses. As the …

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

Motivation In this work we present REINDEER, a novel computational method that performs
indexing of sequences and records their abundances across a collection of datasets. To the …