Related papers: An External-Memory Algorithm for String Graph Cons…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside 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…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
For many algorithmic problems, traditional algorithms that optimise on the number of instructions executed prove expensive on I/Os. Novel and very different design techniques, when applied to these problems, can produce algorithms that are…
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…
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 this paper, we develop semi-external and external memory algorithms for graph partitioning and clustering problems. Graph partitioning and clustering are key tools for processing and analyzing large complex networks. We address both…
Small distributed systems are limited by their main memory to generate massively large graphs. Trivial extension to current graph generators to utilize external memory leads to large amount of random I/O hence do not scale with size. In…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…
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…
In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use…
For decades, computing the LZ factorization (or LZ77 parsing) of a string has been a requisite and computationally intensive step in many diverse applications, including text indexing and data compression. Many algorithms for LZ77 parsing…
The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…
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…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
The Burrows-Wheeler Transform (BWT) is among the most influential discoveries in text compression and DNA storage. It is a reversible preprocessing step that rearranges an $n$-letter string into runs of identical characters (by exploiting…
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…