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Cache Friendly Burrows-Wheeler Inversion

Juha Karkkainen, Simon J. Puglisi
2011 2011 First International Conference on Data Compression, Communications and Processing  
The Burrows-Wheeler transform permutes the symbols of a string such that the permuted string can be compressed effectively with fast, simple techniques.  ...  Inversion of the transform is a bottleneck in practice.  ...  The string L is the Burrows-Wheeler transform of S. An example is given in Figure 1 . Note that F and L (and all other columns in M ) are permutations of S.  ... 
doi:10.1109/ccp.2011.15 dblp:conf/ccp/KarkkainenP11 fatcat:5sbzew2765azzd43b7jqwou7dm

Higher Compression from Burrows-Wheeler Transform for DNA Sequence

Rexline S., Aju Richard, Trujilla Lobo
2017 International Journal of Computer Applications  
In comparison with the existing general purpose compression algorithms, the proposed BWT based method compresses these types of sequences better and at the same time the cost of Burrows-Wheeler Transform  ...  In this paper, the Burrows-Wheeler Transform (BWT) based approaches are explored to compress the biological sequences.  ...  METHODS 2.1 Burrows-Wheeler Transform The Burrows-Wheeler Transform (BWT) was developed by Michael Burrows and David J. Wheeler in 1994 [3] .  ... 
doi:10.5120/ijca2017915261 fatcat:n7bl3a5e2ffyjkoedhv2ch36qq

Parallel algorithms for Burrows–Wheeler compression and decompression

James A. Edwards, Uzi Vishkin
2014 Theoretical Computer Science  
We present work-optimal PRAM algorithms for Burrows-Wheeler compression and decompression of strings over a constant alphabet.  ...  into the stages of the BW compression and decompression problems, bringing out parallelism that was not readily apparent, allowing them to be mapped to elementary parallel routines that have O(log n)-  ...  This transform is also referred to by some authors as the Burrows-Wheeler Transform (BWT).  ... 
doi:10.1016/j.tcs.2013.10.009 fatcat:wamnzzw3inejtdnohv2erbamk4

Faster Average Case Low Memory Semi-External Construction of the Burrows-Wheeler Transform [article]

German Tischler
2016 arXiv   pre-print
The Burrows Wheeler transform has applications in data compression as well as full text indexing.  ...  In this paper we present a new semi external memory algorithm for constructing the Burrows Wheeler transform.  ...  In this case the Burrows-Wheeler transform of t can be obtained from the Burrows-Wheeler transform for α by repeating each symbol k times, e.g. if abc is the Burrows-Wheeler transform for α and we have  ... 
arXiv:1604.06687v1 fatcat:3u2cleqx55awjh44kzeg3bz454

A Multi GPU Read Alignment Algorithm with Model-Based Performance Optimization [chapter]

Aleksandr Drozd, Naoya Maruyama, Satoshi Matsuoka
2013 Lecture Notes in Computer Science  
This paper describes a performance model for read alignment problem, one of the most computationally intensive tasks in bionformatics.  ...  We adapted Burrows Wheeler transform based index to be used with GPUs to reduce overall memory footprint.  ...  This paper shows that using more compact data structures can lead to performance improvement in short read alignment problem.  ... 
doi:10.1007/978-3-642-38718-0_27 fatcat:uxgxoxrnszehpcaapgtd6chrti

Burrows–Wheeler compression: Principles and reflections

Peter Fenwick
2007 Theoretical Computer Science  
After a general description of the Burrows Wheeler Transform and a brief survey of recent work on processing its output, the paper examines the coding of the zero-runs from the MTF recoding stage, an aspect  ...  The paper then proposes some new interpretations and uses of the Burrows Wheeler transform, with new insights and approaches to lossless compression, perhaps including techniques from error correction.  ...  An important example is the Fourier Transform, which converts between time space and frequency space. The Burrows-Wheeler transform similarly transforms from text space to context space.  ... 
doi:10.1016/j.tcs.2007.07.012 fatcat:rsifq647zngobjgifvi22nddru

Space-Efficient Computation of the LCP Array from the Burrows-Wheeler Transform

Nicola Prezza, Giovanna Rosone, Michael Wagner
2019 Annual Symposium on Combinatorial Pattern Matching  
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, σ] can be computed from the Burrows-Wheeler transformed collection in O(n log σ) time using o(n log σ)  ...  An extension of this algorithm that computes also the LCP array of the merged collection processes the data at a rate of 1.48 megabases per second and uses 1.625 Bytes per base in RAM.  ...  Given the Burrows-Wheeler Transform of a text T represented with a wavelet tree, we can compute the LCP array of T in O(n log σ) time using 4n bits of working space on top of the BWT and the LCP.  ... 
doi:10.4230/lipics.cpm.2019.7 dblp:conf/cpm/PrezzaR19 fatcat:catgit4bffdija2vgqodswzlem

Fast Parallel Suffix Array on the GPU [chapter]

Leyuan Wang, Sean Baxter, John D. Owens
2015 Lecture Notes in Computer Science  
We also demonstrate the effectiveness of our implementations in a Burrows-Wheeler transform and a parallel FM index for pattern searching.  ...  The first, skew, makes algorithmic improvements to the previous work of Deo and Keely to achieve a speedup of 1.45x over their work.  ...  Fast Parallel Suffix Array on the GPU  ... 
doi:10.1007/978-3-662-48096-0_44 fatcat:q3dlbm6enrhrboksyni4y5pxqy

Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis

Sophie Schbath, Véronique Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux, Jean-François Gibrat
2012 Journal of Computational Biology  
In this article, we first review the underlying algorithms used in most of the existing mapping tools, and then we compare the performance of nine of these tools on a well controled benchmark built for  ...  On each dataset, we quantified the capacity of the different tools to retrieve all the occurrences of the reads in the reference genome.  ...  We are grateful to the INRA MIGALE bioinformatics platform (http://migale.jouy.inra.fr) for providing computational resources.  ... 
doi:10.1089/cmb.2012.0022 pmid:22506536 pmcid:PMC3375638 fatcat:wwukslo2bjhyvfp4mqgcibyewi

Space-Efficient Construction of Compressed Suffix Trees [article]

Nicola Prezza, Giovanna Rosone
2019 arXiv   pre-print
We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space.  ...  We also consider the problem of merging BWTs of string collections, and provide a solution running in O(nlogσ) time and using just o(nlogσ) bits of working space.  ...  If Open[l − (i − Theorem 6 . 6 Given the Burrows-Wheeler Transforms of two collections S 1 and S 2 of total length n on alphabet [1, σ], we can compute the Document Array of S 1 ∪ S 2 in O(n log σ) time  ... 
arXiv:1908.04686v1 fatcat:nug7mrmbcrg5hiyjucelb3npae

Succinct Suffix Arrays Based on Run-Length Encoding [chapter]

Veli Mäkinen, Gonzalo Navarro
2005 Lecture Notes in Computer Science  
In addition, we prove a close relationship between the kth order entropy of the text and some regularities that show up in their suffix arrays and in the Burrows-Wheeler transform of T .  ...  Several remarkable self-indexes have been developed in recent years. Many of those take space proportional to nH 0 or nH k bits, where H k is the kth order empirical entropy of T .  ...  ) and the number of runs of equal letters in the Burrows-Wheeler transformed text T bwt (Section 2.2).  ... 
doi:10.1007/11496656_5 fatcat:d6bg2rynjbb27ezwbm6vkrx7fq

Compression, Indexing, and Retrieval for Massive String Data [chapter]

Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter
2010 Lecture Notes in Computer Science  
notions of relevance in the reporting of query answers.  ...  In this invited presentation, we discuss some breakthroughs in compressed data structures over the course of the last decade that have significantly reduced the space requirements for fast text and document  ...  In parallel with the development of the CSA, Ferragina and Manzini introduced the elegant FM-index [19, 20] , based upon the Burrows-Wheeler transform (BWT)[7, 50] data compressor.  ... 
doi:10.1007/978-3-642-13509-5_24 fatcat:yai4yylbdfhqxm7n65m7vw4lli

Prospects and limitations of full-text index structures in genome analysis

M. Vyverman, B. De Baets, V. Fack, P. Dawyndt
2012 Nucleic Acids Research  
results in the life sciences.  ...  Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs.  ...  The authors also like to acknowledge the members of the Nucleotides to Networks next-generation sequencing discussion group, in particular Yao-Cheng Lin and Lieven Sterck, for their helpful comments in  ... 
doi:10.1093/nar/gks408 pmid:22584621 pmcid:PMC3424560 fatcat:5sfziui7ujhfzcqhcukbi4utjq

Compressing and Indexing Aligned Readsets [article]

Travis Gagie, Garance Gourdel, Giovanni Manzini
2021 arXiv   pre-print
Next, we compute the eXtended Burrows-Wheeler Transform (XBWT) of the resulting labelled tree and build a compressed full-text index on that.  ...  Following the established practice for datasets with many repetitions, we compare different full-text indices by looking at the number of runs in the transformed strings.  ...  Notably, last year Gagie, Navarro and Prezza [12] showed how to support fast locating queries with the run-length compressed Burrows-Wheeler Transform (RLBWT) while still using only O(ρ) space, where  ... 
arXiv:1809.07320v5 fatcat:5ogzid3dj5dejiau3grfvdi4my

Using Arithmetic Coding for Reduction of Resulting Simulation Data Size on Massively Parallel GPGPUs [chapter]

Ana Balevic, Lars Rockstroh, Marek Wroblewski, Sven Simon
2008 Lecture Notes in Computer Science  
The popularity of parallel platforms, such as general purpose graphics processing units (GPGPUs) for large-scale simulations is rapidly increasing, however the I/O bandwidth and storage capacity of these  ...  massively-parallel cards remain the major bottle necks.  ...  methods and various transforms such as Burrows-Wheeler Transform (BWT), that are now a part of widely used compression utilities, such as Zip, RAR, etc as well as image and video codecs.  ... 
doi:10.1007/978-3-540-87475-1_40 fatcat:43xxqkrpfreo7boigcqoe7g4pq
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