Related papers: Compressing and Indexing Aligned Readsets
We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…
The Burrows-Wheeler transform (BWT) is a string transformation that enhances string indexing and compressibility. Cotumaccio and Prezza [SODA '21] extended this transformation to nondeterministic finite automata (NFAs) through…
Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…
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…
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…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
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…
A parameterized string (p-string) is a string over an alphabet $(\Sigma_{s} \cup \Sigma_{p})$, where $\Sigma_{s}$ and $\Sigma_{p}$ are disjoint alphabets for static symbols (s-symbols) and for parameter symbols (p-symbols), respectively.…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
Text datasets can be represented using models that do not preserve text structure, or using models that preserve text structure. Our hypothesis is that depending on the dataset nature, there can be advantages using a model that preserves…
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…
In many modern applications, including analysis of gene expression and text documents, the data are noisy, high-dimensional, and unordered--with no particular meaning to the given order of the variables. Yet, successful learning is often…
Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…
Text retrieval using learned sparse representations of queries and documents has, over the years, evolved into a highly effective approach to search. It is thanks to recent advances in approximate nearest neighbor search-with the emergence…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
A labeled tree (or a trie) is a natural generalization of a string, which can also be seen as a compact representation of a set of strings. This paper considers the labeled tree indexing problem, and provides a number of new results on…
We show that the compressed suffix array and the compressed suffix tree for a string of length $n$ over an integer alphabet of size $\sigma\leq n$ can both be built in $O(n)$ (randomized) time using only $O(n\log\sigma)$ bits of working…
Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…