Related papers: Tailoring r-index for metagenomics
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
Gagie, Navarro and Prezza's $r$-index (SODA, 2018) promises to speed up DNA alignment and variation calling by allowing us to index entire genomic databases, provided certain obstacles can be overcome. In this paper we first strengthen and…
Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, in…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…
Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in modern metagenomic projects, recent tools [4, 39] rely on the…
A central task in string processing is text indexing, where the goal is to preprocess a text (a string of length $n$) into an efficient index (a data structure) supporting queries about the text. Cole, Gottlieb, and Lewenstein (STOC 2004)…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
Haplotype Inference is a challenging problem in bioinformatics that consists in inferring the basic genetic constitution of diploid organisms on the basis of their genotype. This information allows researchers to perform association studies…
We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…
In this paper we study lower bounds for the fundamental problem of text indexing with mismatches and differences. In this problem we are given a long string of length $n$, the "text", and the task is to preprocess it into a data structure…
Consider an input text string T[1,N] drawn from an unbounded alphabet. We study partial computation in suffix-based problems for Data Compression and Text Indexing such as (I) retrieve any segment of K<=N consecutive symbols from the…
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 texts…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
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…
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based)…
The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The…