3 citations · 8 across the 8 of their papers we have counts for
8 papers · 1 filter
Adaptive encodings for small and fast compressed suffix arrays
Diego Díaz-Domínguez, Veli Mäkinen
Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Tra…
Prefix-free parsing for merging big BWTs
Diego Diaz-Dominguez, Travis Gagie, Veronica Guerrini +5
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset c…
Efficient terabyte-scale text compression via stable local consistency and parallel grammar processing
Diego Diaz-Dominguez
We present a highly parallelizable text compression algorithm that scales efficiently to terabyte-sized datasets. Our method builds on locally consistent grammars, a lightweight fo…
Computing all-vs-all MEMs in run-length encoded collections of HiFi reads
Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to…
Efficient Construction of the BWT for Repetitive Text Using String Compression
Diego Díaz-Domínguez, Gonzalo Navarro
We present a new semi-external algorithm that builds the Burrows--Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression t…
An Index for Sequencing Reads Based on The Colored de Bruijn Graph
Diego Diaz-Domínguez
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we enco…
Simulating the DNA String Graph in Succinct Space
Diego Díaz-Domínguez, Travis Gagie, Gonzalo Navarro
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are…
Assembling Omnitigs using Hidden-Order de Bruijn Graphs
Diego Díaz-Domínguez, Djamal Belazzougui, Travis Gagie +3
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there ma…