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A Framework for Space-Efficient String Kernels

Djamal Belazzougui, Fabio Cunial
2017 Algorithmica  
Versatile succinct representations of the bidirectional Burrows-Wheeler transform. ESA 2013. D. Belazzougui, G. Navarro, D. Valenzuela. Improved compressed indexes for full-text document retrieval.  ...  O(n log log σ) Burrows-Wheeler tr. [1] D. Belazzougui. Linear time construction of compressed text indices in compact space. STOC 2014. [2] D. Belazzougui, G. Navarro, D. Valenzuela.  ... 
doi:10.1007/s00453-017-0286-4 fatcat:e2r44hskgrhfvo4f6who3fphgi

25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241)

Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Jens Stoye, Michael Wagner
2019 Dagstuhl Reports  
Dagstuhl Seminar 19241 ("25 Years of the Burrows-Wheeler Transform") took place from June 10th to 14th, 2019, and was attended by 45 people from 13 countries and the three fields of Algorithms and Data  ...  Feedback was generally positive and we are confident the seminar fostered interdisciplinary connections and will eventually result in noteworthy joint publications. License Creative Commons BY 3.0  ...  We present an index data structure for the bijective Burrows-Wheeler transform [1] . The index data structure is based on the FM index [2] .  ... 
doi:10.4230/dagrep.9.6.55 dblp:journals/dagstuhl-reports/GagieMNS19 fatcat:vw3nruzqkzbrdi3rpxpqtjkosa

Wavelet Trees for All [chapter]

Gonzalo Navarro
2012 Lecture Notes in Computer Science  
There exists a (1D) RMQ structure that, on array A[1, n] of numbers, Requires 2n + o(n) bits of space. Answers queries in constant time. Does not access A.  ...  Discrete Grids Use a wavelet tree for the points. Store the values aligned to the root bitmap, in V [1, n]. We store a one-dimensional RMQ structure per wavelet tree node, for V v [1, n v ].  ...  and visibility reduce A B B B B B B B B C C C C C C C C C D D D D D D D D Full-text IndexesA way to simulate the suffix array A[1, n] in little space uses the Burrows-Wheeler Transform (BWT) of T  ... 
doi:10.1007/978-3-642-31265-6_2 fatcat:najqyrywlrezdofzr7c674olnm

Wavelet trees for all

Gonzalo Navarro
2014 Journal of Discrete Algorithms  
There exists a (1D) RMQ structure that, on array A[1, n] of numbers, Requires 2n + o(n) bits of space. Answers queries in constant time. Does not access A.  ...  Discrete Grids Use a wavelet tree for the points. Store the values aligned to the root bitmap, in V [1, n]. We store a one-dimensional RMQ structure per wavelet tree node, for V v [1, n v ].  ...  and visibility reduce A B B B B B B B B C C C C C C C C C D D D D D D D D Full-text IndexesA way to simulate the suffix array A[1, n] in little space uses the Burrows-Wheeler Transform (BWT) of T  ... 
doi:10.1016/j.jda.2013.07.004 fatcat:43562tjtr5fajgr4nue4zcteei

Computation over Compressed Structured Data (Dagstuhl Seminar 16431)

Philip Bille, Markus Lohrey, Sebastian Maneth, Gonzalo Navarro, Marc Herbstritt
2017 Dagstuhl Reports  
This report documents the program and the outcomes of Dagstuhl Seminar 16431 "Computation over Compressed Structured Data".  ...  We plan to combine the recently proposed GLOUDS representation [1] with DSM, a technique used to compress Web and social graphs by exploiting the presence of bicliques and dense subgraphs [2].  ...  Since GLOUDS benefits from a representation with fewer edges per node and DSM reduces the number of edges from m * n to m + n when representing an (m, n)-biclique, we believe the combination can lead to  ... 
doi:10.4230/dagrep.6.10.99 dblp:journals/dagstuhl-reports/BilleLMN16 fatcat:jel4wyc2gje6thmu5zj7aryofu

Linear-time string indexing and analysis in small space [article]

Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
2016 arXiv   pre-print
on the Burrows-Wheeler transform (BWT) have been developed, all taking an amount of space that is close to the input size in bits.  ...  The field of succinct data structures has flourished over the last 16 years.  ...  Acknowledgement The authors wish to thank Travis Gagie for explaining the data structure built in Lemma 33, as well as for valuable comments and encouragements, Gonzalo Navarro for explaining the algorithm  ... 
arXiv:1609.06378v1 fatcat:nwtoh4rvmjcjle2oe4u3c3byie

GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment [article]

Mikko Rautiainen, Tobias Marschall
2019 bioRxiv   pre-print
Compared to state-of-the-art tools, GraphAligner is 12x faster and uses 5x less memory, making it as efficient as aligning reads to linear reference genomes.  ...  Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pan-genome graph.  ...  Availability of data and materials  ... 
doi:10.1101/810812 fatcat:mksvk7jfyngyte4n6esa54qb4q

GraphAligner: rapid and versatile sequence-to-graph alignment

Mikko Rautiainen, Tobias Marschall
2020 Genome Biology  
Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory.  ...  Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph.  ...  The source code of GraphAligner is available on GitHub [67] . The source code of GraphAligner version 1.0.11 used in the experiments is available on Zenodo [68]  ... 
doi:10.1186/s13059-020-02157-2 pmid:32972461 fatcat:sxz4jkj4crgdxi2oc4h4kr7iem

Time- and Space-Efficient Regular Path Queries on Graphs [article]

Diego Arroyuelo, Aidan Hogan, Gonzalo Navarro, Javiel Rojas-Ledesma
2021 arXiv   pre-print
We combine a bit-parallel simula-tion of the Glushkov automaton of the regular expression with thering index introduced by Arroyuelo et al., exploiting its wavelettree representation of the triples in  ...  order to efficiently reach thestates of the product graph that are relevant for the query.  ...  The concatenation 𝐿 o • 𝐿 s • 𝐿 p is indeed the Burrows-Wheeler Transform (BWT) [9] of the concatenation of all the triples (with some tweaks, see the original article [4] for details).  ... 
arXiv:2111.04556v1 fatcat:jmnlkleovbcq3gxu3hdm63hvgu

Sequence to graph alignment : theory, practice and applications [article]

Mikko Rautiainen, Universität Des Saarlandes
2020
One representation of pangenomes is the sequence graph or the pangenome graph, which uses a graph format to represent genetic diversity.  ...  To show the utility of GraphAligner, I present a long read genotyping pipeline, and an error correction pipeline that outperforms existing tools by a factor of two in correction accuracy and an order of  ...  A Wheeler graph is essentially a generalization of the Burrows-Wheeler transform to graphs, and any linear string can be considered a linear Wheeler graph.  ... 
doi:10.22028/d291-32061 fatcat:vvpwnf6ejvbc5oeabusfflxqc4

Dagstuhl Reports, Volume 9, Issue 6, June 2019, Complete Issue [article]

2020
The vision of Real VR is enabling to experience movies, concerts, even live sports events in HMDs with the sense of immersion of really "being-there", unattainable by today's technologies.  ...  the state-of-the-art, current challenges, as well as promising future research directions in Real VR.  ...  In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced.  ... 
doi:10.4230/dagrep.9.6 fatcat:3w3rearmjrdejkbazhpjqmucde

Approaches to genome analysis through the application of graph theory

Alice M. Kaye
2021
Over the past twenty years the cost of genome sequencing has dropped from a prohibitive amount of hundreds of millions of dollars, to just a few thousand dollars.  ...  Partial, ad-hoc solutions, such as the introduction of alternative sequences for sections of the genome, have provided a stopgap but fail to fully represent the wealth of information now known about the  ...  Burrows Wheeler Transform In situations where there is a very small alphabet size compared to the length of the string, a suffix array can occupy more space than the original string.  ... 
doi:10.14288/1.0401888 fatcat:hy7riaj4ajbsbhkcjr3pkftb7a

Approximate string matching for high-throughput sequencing [article]

Enrico Siragusa, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
2015
The ability to assess the content of a DNA sample at base-level resolution opens the way to a myriad of applications, including individual genotyping and assessment of large structural variations, measurement  ...  To the best of my knowledge, this is the first study providing a comprehensive exposition, implementation and evaluation of such methods.  ...  Succinct full-text indices The Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994 ] is a transformation de ining a permutation of an input string.  ... 
doi:10.17169/refubium-15562 fatcat:opflq33mv5ewbkxkaokacdwlx4