8 citations · 13 across the 6 of their papers we have counts for
8 papers · 1 filter
Computing Maximal Unique Matches with the r-index
Sara Giuliani, Giuseppe Romana, Massimiliano Rossi
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference ge…
RLBWT Tricks
Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi
Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so rel…
Computing the original eBWT faster, simpler, and with less memory
Christina Boucher, Davide Cenzato, Zsuzsanna Lipták +2
Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings, however, since this introduction, it has been used more generally to desc…
PHONI: Streamed Matching Statistics with Multi-Genome References
Christina Boucher, Travis Gagie, Tomohiro I +6
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic data…
PFP Data Structures
Christina Boucher, Ondřej Cvacho, Travis Gagie +4
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 a…
Tailoring r-index for metagenomics
Dustin Cobas, Veli Mäkinen, Massimiliano Rossi
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metageno…
Pattern Discovery in Colored Strings
Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of c…
Bubble-Flip -- A New Generation Algorithm for Prefix Normal Words
Ferdinando Cicalese, Zsuzsanna Lipták, Massimiliano Rossi
We present a new recursive generation algorithm for prefix normal words. These are binary strings with the property that no substring has more 1s than the prefix of the same length…