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07/05/2023
Compressibility measures for two-dimensional data
In this paper we extend to two-dimensional data two recently introduced ...
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01/13/2023
Computing matching statistics on Wheeler DFAs
Matching statistics were introduced to solve the approximate string matc...
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08/21/2022
Teaching the Burrows-Wheeler Transform via the Positional Burrows-Wheeler Transform
The Burrows-Wheeler Transform (BWT) is often taught in undergraduate cou...
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05/11/2022
A New Class of String Transformations for Compressed Text Indexing
Introduced about thirty years ago in the field of Data Compression, the ...
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03/28/2022
Improving Matrix-vector Multiplication via Lossless Grammar-Compressed Matrices
As nowadays Machine Learning (ML) techniques are generating huge data co...
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11/11/2020
PHONI: Streamed Matching Statistics with Multi-Genome References
Computing the matching statistics of patterns with respect to a text is ...
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09/05/2020
Space efficient merging of de Bruijn graphs and Wheeler graphs
The merging of succinct data structures is a well established technique ...
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06/21/2020
PFP Data Structures
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a p...
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10/16/2019
Tree-Shape Grammars for Random Access
Shape grammars are well known in the graphics and design communities but...
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08/04/2019
Matching reads to many genomes with the r-index
The r-index is a tool for compressed indexing of genomic databases for e...
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07/04/2019
The Alternating BWT: an algorithmic perspective
The Burrows-Wheeler Transform (BWT) is a word transformation introduced ...
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06/03/2019
Rpair: Rescaling RePair with Rsync
Data compression is a powerful tool for managing massive but repetitive ...
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05/30/2019
Inducing the Lyndon Array
In this paper we propose a variant of the induced suffix sorting algorit...
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03/04/2019
Lightweight merging of compressed indices based on BWT variants
In this paper we propose a flexible and lightweight technique for mergin...
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02/07/2019
Space-efficient merging of succinct de Bruijn graphs
We propose a new algorithm for merging succinct representations of de Br...
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02/04/2019
A New Class of Searchable and Provably Highly Compressible String Transformations
The Burrows-Wheeler Transform is a string transformation that plays a fu...
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11/16/2018
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
While short read aligners, which predominantly use the FM-index, are abl...
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05/17/2018
External memory BWT and LCP computation for sequence collections with applications
We propose an external memory algorithm for the computation of the BWT a...
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03/29/2018
Prefix-Free Parsing for Building Big BWTs
High-throughput sequencing technologies have led to explosive growth of ...
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10/27/2017