Related papers: Indexing arbitrary-length $k$-mers in sequencing r…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
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…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…
Minimizers are sampling schemes with numerous applications in computational biology. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a linear order $\rho$ on strings of length $k$ (also…
Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still…
We design the first learned index that solves the dictionary problem with time and space complexity provably better than classic data structures for hierarchical memories, such as B-trees, and modern learned indexes. We call our solution…
The extraction of k-mers from sequencing reads is an important task in many bioinformatics applications, such as all DNA sequence analysis methods based on de Bruijn graphs. These methods tend to be more accurate when the used k-mers are…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and…
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…
In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abundance on various phenomena, such as the size and repeat…
Overlap is a common phenomenon seen when structural components of a digital object are neither disjoint nor nested inside each other. Overlapping components resist reduction to a structural hierarchy, and tree-based indexing and query…
The class of Gaussian Process (GP) methods for Temporal Difference learning has shown promise for data-efficient model-free Reinforcement Learning. In this paper, we consider a recent variant of the GP-SARSA algorithm, called Sparse…
A basic task in bioinformatics is the counting of $k$-mers in genome strings. The $k$-mer counting problem is to build a histogram of all substrings of length $k$ in a given genome sequence. We present the open source $k$-mer counting…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Estimating the abundances of all $k$-mers in a set of biological sequences is a fundamental and challenging problem with many applications in biological analysis. While several methods have been designed for the exact or approximate…
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…
This paper provides a comprehensive survey of data structures for representing k-mer sets, which are fundamental in high-throughput sequencing analysis. It categorizes the methods into two main strategies: those using fingerprinting and…