Related papers: A massively parallel algorithm for constructing th…
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…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
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…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings, however, since this introduction, it has been used more generally to describe any BWT of a collection of strings and the fundamental…
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
We present a new semi-external algorithm that builds the Burrows--Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression techniques to reduce computational costs when the input is…
The effective use of parallel computing resources to speed up algorithms in current multi-core parallel architectures remains a difficult challenge, with ease of programming playing a key role in the eventual success of various parallel…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
Finite-state transducers (FSTs) are frequently used in speech recognition. Transducer composition is an essential operation for combining different sources of information at different granularities. However, composition is also one of the…
Burrows-Wheeler transform (BWT) is an invertible text transformation that, given a text $T$ of length $n$, permutes its symbols according to the lexicographic order of suffixes of $T$. BWT is one of the most heavily studied algorithms in…
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,…
Sequential computation is well understood but does not scale well with current technology. Within the next decade, systems will contain large numbers of processors with potentially thousands of processors per chip. Despite this, many…
We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we…
Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…