Related papers: Resolution of the Burrows-Wheeler Transform Conjec…
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…
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…
Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Transform (BWT) with suffix array sampling to achieve space…
The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…
In this paper we study the number $r_{bwt}$ of equal-letter runs produced by the Burrows-Wheeler transform ($BWT$) when it is applied to purely morphic finite words, which are words generated by iterating prolongable morphisms. Such a…
The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…
We study how the application of injective morphisms affects the number $r$ of equal-letter runs in the Burrows-Wheeler Transform (BWT). This parameter has emerged as a key repetitiveness measure in compressed indexing. We focus on the…
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. Let $n$ be the text length and $\sigma$ be the alphabet size.…
Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory…
In this paper we propose a flexible and lightweight technique for merging compressed indices based on variants of Burrows-Wheeler transform (BWT), thus addressing the need for algorithms that compute compressed indices over large…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in $O (r)$ space and $O ((r + L) \log (m + n))$ time, where $m$ and $n$ are the…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…
In this article we extend the elegant in-place Burrows-Wheeler transform (BWT) algorithm proposed by Crochemore et al. (Crochemore et al., 2015). Our extension is twofold: we first show how to compute simultaneously the longest common…
We study the impact that string reversal can have on several repetitiveness measures. First, we exhibit an infinite family of strings where the number, $r$, of runs in the run-length encoding of the Burrows--Wheeler transform (BWT) can…
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
We prove that for every integer $n > 0$ and for every alphabet $\Sigma_k$ of size $k \geq 3$, there exists a necklace of length $n$ whose Burrows-Wheeler Transform (BWT) is completely unclustered, i.e., it consists of exactly $n$ runs with…
A weight based dynamic compression method has recently been proposed, which is especially suitable for the encoding of files with locally skewed distributions. Its main idea is to assign larger weights to closer to be encoded symbols by…