Related papers: Computing the BWT and LCP array of a Set of String…
The Burrows Wheeler transform has applications in data compression as well as full text indexing. Despite its important applications and various existing algorithmic approaches the construction of the transform for large data sets is still…
The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the…
The compression of highly repetitive strings (i.e., strings with many repetitions) has been a central research topic in string processing, and quite a few compression methods for these strings have been proposed thus far. Among them, an…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the…
The suffix array, perhaps the most important data structure in modern string processing, is often augmented with the longest common prefix (LCP) array which stores the lengths of the LCPs for lexicographically adjacent suffixes of a string.…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…
It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…
Suffix arrays and LCP arrays are one of the most fundamental data structures widely used for various kinds of string processing. We consider two problems for a read-only string of length $N$ over an integer alphabet $[1, \dots, \sigma]$ for…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…
The Burrows-Wheeler transform (BWT) is a well studied text transformation widely used in data compression and text indexing. The BWT of two strings can also provide similarity measures between them, based on the observation that the more…
In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
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 can be broken down into small datasets that are not very…
Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which…
For a partial word $w$ the longest common compatible prefix of two positions $i,j$, denoted $lccp(i,j)$, is the largest $k$ such that $w[i,i+k-1]\uparrow w[j,j+k-1]$, where $\uparrow$ is the compatibility relation of partial words (it is…
The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the…