Filters








1,246 Hits in 8.7 sec

A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications [article]

Adam M Novak, Erik Garrison, Benedict Paten
2016 bioRxiv   pre-print
We present a generalization of the Positional Burrows-Wheeler Transform (PBWT) to genome graphs, which we call the gPBWT.  ...  As a demonstration, we use the gPBWT to quickly count the number of haplotypes consistent with random walks in a genome graph, and with the paths taken by mapped reads; results suggest that haplotype consistency  ...  Acknowledgements We would like to thank Richard Durbin for inspiration and David Haussler for his extremely helpful comments on the manuscript.  ... 
doi:10.1101/051409 fatcat:otb5aec2wjfpdaoetcb5fuzq7u

A Graph Extension of the Positional Burrows-Wheeler Transform and Its Applications [chapter]

Adam M. Novak, Erik Garrison, Benedict Paten
2016 Lecture Notes in Computer Science  
We present a generalization of the Positional Burrows-Wheeler Transform (PBWT) to genome graphs, which we call the gPBWT.  ...  As a demonstration, we use the gPBWT to quickly count the number of haplotypes consistent with random walks in a genome graph, and with the paths taken by mapped reads; results suggest that haplotype consistency  ...  Acknowledgements We would like to thank Richard Durbin for inspiration and David Haussler for his extremely helpful comments on the manuscript.  ... 
doi:10.1007/978-3-319-43681-4_20 fatcat:rpuutyx3vra7xkuruhjvkx3rxi

A graph extension of the positional Burrows–Wheeler transform and its applications

Adam M. Novak, Erik Garrison, Benedict Paten
2017 Algorithms for Molecular Biology  
We present a generalization of the Positional Burrows-Wheeler Transform (PBWT) to genome graphs, which we call the gPBWT.  ...  As a demonstration, we use the gPBWT to quickly count the number of haplotypes consistent with random walks in a genome graph, and with the paths taken by mapped reads; results suggest that haplotype consistency  ...  Acknowledgements We would like to thank Richard Durbin for inspiration and David Haussler for his extremely helpful comments on the manuscript.  ... 
doi:10.1186/s13015-017-0109-9 pmid:28702075 pmcid:PMC5505026 fatcat:x2cb2sw7obfejarium452dxca4

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  ...  There were four talks and a panel session for each field.  ...  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

Subpath Queries on Compressed Graphs: A Survey

Nicola Prezza
2021 Algorithms  
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text T, pre-process it off-line so that, later, we can quickly count and locate the occurrences of  ...  In turn, since finite state automata can be considered as a particular case of labeled graphs, these findings created a bridge between the fields of compressed indexing and regular language theory, ultimately  ...  As far as graph compression is concerned, it is plausible that new powerful graph compression schemes will emerge from developments in the field: an extension of the run-length Burrows Wheeler transform  ... 
doi:10.3390/a14010014 fatcat:leysuxakfbdofnnpjnh5xphzcq

Subpath Queries on Compressed Graphs: a Survey [article]

Nicola Prezza
2020 arXiv   pre-print
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text T, pre-process it off-line so that, later, we can quickly count and locate the occurrences of  ...  In turn, since finite state automata can be considered as a particular case of labeled graphs, these findings created a bridge between the fields of compressed indexing and regular language theory, ultimately  ...  As far as graph compression is concerned, it is plausible that new powerful graph compression schemes will emerge from developments in the field: an extension of the run-length Burrows Wheeler transform  ... 
arXiv:2011.10008v2 fatcat:nbx6tdyurbfexkojuuyzmpr4wu

Prefix-free parsing for building large tunnelled Wheeler graphs [article]

Adrián Goga, Andrej Baláž
2022 arXiv   pre-print
Wheeler graphs (WGs) are a general framework encompassing several indexes based on the Burrows-Wheeler transform (BWT), such as the FM-index.  ...  Wheeler graphs admit a succinct representation which can be further compacted by employing the idea of tunnelling, which exploits redundancies in the form of parallel, equally-labelled paths called blocks  ...  Acknowledgements We want to thank Travis Gagie for the conception of the idea during his data structures course and helpful remarks throughout the realisation of this project.  ... 
arXiv:2206.15097v1 fatcat:q3qvf76hcfagfcmjhyvdf33nde

Resolving Load Balancing Issues in BWA on NUMA Multicore Architectures [chapter]

Charlotte Herzeel, Thomas J. Ashby, Pascal Costanza, Wolfgang De Meuter
2014 Lecture Notes in Computer Science  
This is because the current parallelisation strategy does not take into account the load imbalance that is inherent to the properties of the data being aligned, e.g. varying read lengths and numbers of  ...  We show that rewriting the parallel section using Cilk removes the load imbalance, resulting in a factor two performance improvement over the original BWA.  ...  This work is funded by Intel, Janssen Pharmaceutica and by the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT).  ... 
doi:10.1007/978-3-642-55195-6_21 fatcat:oinok3gqn5gllavaxrmujz4pnu

Indexing Finite Language Representation of Population Genotypes [chapter]

Jouni Sirén, Niko Välimäki, Veli Mäkinen
2011 Lecture Notes in Computer Science  
The finite automaton is indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences.  ...  The size of the index stays limited, because of the high similarity of individual genomes. The index finds applications in variation calling and in primer design.  ...  Acknowledgements We wish to thank Eric Rivals for pointing out recombination hotspots and Riku Katainen for running the variation calling experiment.  ... 
doi:10.1007/978-3-642-23038-7_23 fatcat:fqqyijt2obho7cdwoth35rdpia

Fully-functional bidirectional Burrows-Wheeler indexes [article]

Fabio Cunial, Djamal Belazzougui
2019 arXiv   pre-print
Given a string T on an alphabet of size σ, we describe a bidirectional Burrows-Wheeler index that takes O(|T|logσ) bits of space, and that supports the addition and removal of one character, on the left  ...  We also describe an index that supports bidirectional addition and removal in O(loglog|T|) time, and that occupies a number of words proportional to the number of left and right extensions of the maximal  ...  representations, like the affix array [39] and the bidirectional Burrows-Wheeler transform (BWT) [35] .  ... 
arXiv:1901.10165v2 fatcat:jix3wf2qsbhsne3zj5jg6zcmye

Fully-Functional Bidirectional Burrows-Wheeler Indexes and Infinite-Order De Bruijn Graphs

Djamal Belazzougui, Fabio Cunial, Michael Wagner
2019 Annual Symposium on Combinatorial Pattern Matching  
Given a string T on an alphabet of size σ, we describe a bidirectional Burrows-Wheeler index that takes O(|T | log σ) bits of space, and that supports the addition and removal of one character, on the  ...  We also describe an index that supports bidirectional addition and removal in O(log log |T |) time, and that takes a number of words proportional to the number of left and right extensions of the maximal  ...  Acknowledgements We thank Martin Bundgaard for motivating the contract operation, Rodrigo Canovas for discussions about bidirectional indexes, Gene Myers for discussions about PacBio CCS reads, and German  ... 
doi:10.4230/lipics.cpm.2019.10 dblp:conf/cpm/BelazzouguiC19 fatcat:xsgwqm5gabcqhpgrb7jyamygqa

Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding

Bastien Cazaux, Eric Rivals, Michael Wagner
2019 Annual Symposium on Combinatorial Pattern Matching  
The most prominent example of such data structures is the Burrows-Wheeler Transform (BWT), a reversible permutation of a text that improves its compressibility.  ...  A similar data structure, the eXtended Burrows-Wheeler Transform (XBW), is able to index a tree labelled with alphabet symbols.  ...  This induces a link between the Burrows-Wheeler Transform and the eXtended Burrows-Wheeler Transform, via the Aho-Corasick automaton.  ... 
doi:10.4230/lipics.cpm.2019.24 dblp:conf/cpm/CazauxR19 fatcat:bcv7uv63ifhx7eidm2tbb745pi

Computational methods for differentially expressed gene analysis from RNA-Seq: an overview [article]

Juliana Costa-Silva, Douglas S. Domingues, David Menotti, Mariangela Hungria, Fabricio M Lopes
2021 arXiv   pre-print
This paper presents a review of differential expression analysis pipeline, addressing its steps and the respective objectives, the principal methods available in each step and their properties, bringing  ...  The steps for the computational analysis of these data include many data types and file formats, and a wide variety of computational tools that can be applied alone or together as pipelines.  ...  Name Algorithm Year Reference BWA Burrows-Wheeler Transform 2009 [39] RUM Burrows-Wheeler Transform 2011 [40] Bowtie2 Burrows-Wheeler Transform 2012 [41] BWBBLE Burrows-Wheeler Transform  ... 
arXiv:2109.03625v1 fatcat:izqrrofprjd2zml6yqykklqjh4

From first principles to the Burrows and Wheeler transform and beyond, via combinatorial optimization

R. Giancarlo, A. Restivo, M. Sciortino
2007 Theoretical Computer Science  
The Burrows and Wheeler transform ( bwt) (cf. [M. Burrows, D.  ...  The results presented here indicate that a key feature of the Burrows and Wheeler transform seems to be, besides compressibility, the existence of efficient algorithms for its computation and inversion  ...  The Burrows-Wheeler transform provides a method able to compute a very special lcp-optimal induced word permutation that has two key properties: it is very fast to compute and it is easy to invert.  ... 
doi:10.1016/j.tcs.2007.07.019 fatcat:vcpnsui7fzf4rdtfqp2rieyz7i

Multi de Bruijn sequences

Glenn Tesler
2017 Journal of Combinatorics  
This uses an extension of the Burrows-Wheeler Transform due to Mantaci et al, and generalizes a result by Higgins for the case m=1.  ...  We generalize the notion of a de Bruijn sequence to a "multi de Bruijn sequence": a cyclic or linear sequence that contains every k-mer over an alphabet of size q exactly m times.  ...  called de Bruijn sets and showed how to generate them using an extension [13, 14] of the Burrows-Wheeler Transformation (BWT) [1] .  ... 
doi:10.4310/joc.2017.v8.n3.a3 fatcat:ztx5jj4gvjhjzges7zab6ixhsy
« Previous Showing results 1 — 15 out of 1,246 results