Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …

Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …

Computational pan-genome analysis has emerged from the rapid increase of available
genome sequencing data. Starting from a microbial pan-genome, the concept has spread to …

Self-indexes are able to represent a text asymptotically within the information-theoretic lower
bound under the k th order entropy model and offer access to any text substring and indexed …

We consider the problem of computing the Maximal Exact Matches (MEMs) of a given
pattern $ P [1.. m] $ on a large repetitive text collection $ T [1.. n] $, which is represented as a …

Domain encoding is a common technique to compress the columns of a column store and to
accelerate many types of queries at the same time. It is based on the assumption that most …

The combination of incessant advances in sequencing technology producing large amounts
of data and innovative bioinformatics approaches, designed to cope with this data flood, has …

We describe succinct and compact representations of the bidirectional bwt of a string s∈ Σ*
which provide increasing navigation power and a number of space-time tradeoffs. One such …

Prefix-free parsing (PFP) was introduced by Boucher et al.(2019) as a preprocessing step to
ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given …

Motivated by challenges in pangenomic read alignment, we propose a generalization of
Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text T [1.. n] and an …