When less is more: sketching with minimizers in genomics
The exponential increase in sequencing data calls for conceptual and computational
advances to extract useful biological insights. One such advance, minimizers, allows for …
advances to extract useful biological insights. One such advance, minimizers, allows for …
BWT construction and search at the terabase scale
H Li - Bioinformatics, 2024 - academic.oup.com
Abstract Motivation Burrows–Wheeler Transform (BWT) is a common component in full-text
indices. Initially developed for data compression, it is particularly powerful for encoding …
indices. Initially developed for data compression, it is particularly powerful for encoding …
Efficient and robust search of microbial genomes via phylogenetic compression
Comprehensive collections approaching millions of sequenced genomes have become
central information sources in the life sciences. However, the rapid growth of these …
central information sources in the life sciences. However, the rapid growth of these …
GIN-TONIC: non-hierarchical full-text indexing for graph genomes
Ü Öztürk, M Mattavelli, P Ribeca - NAR Genomics and …, 2024 - academic.oup.com
This paper presents a new data structure, GIN-TONIC (G raph IN dexing T hrough O ptimal N
ear I nterval C ompaction), designed to index arbitrary string-labelled directed graphs …
ear I nterval C ompaction), designed to index arbitrary string-labelled directed graphs …
Improved pangenomic classification accuracy with chain statistics
Compressed full-text indexes enable efficient sequence classification against a pangenome
or tree-of-life index. Past work on compressed-index classification used matching statistics …
or tree-of-life index. Past work on compressed-index classification used matching statistics …
Mumemto: efficient maximal matching across pangenomes
VS Shivakumar, B Langmead - bioRxiv, 2025 - biorxiv.org
Aligning genomes into common coordinates is central to pangenome analysis and
construction, but it is also computationally expensive. Multi-sequence maximal unique …
construction, but it is also computationally expensive. Multi-sequence maximal unique …
Differential quantification of alternative splicing events on spliced pangenome graphs
Pangenomes are becoming a powerful framework to perform many bioinformatics analyses
taking into account the genetic variability of a population, thus reducing the bias introduced …
taking into account the genetic variability of a population, thus reducing the bias introduced …
[PDF][PDF] MIOV: Reordering MOVI for even better locality
arXiv:2407.18956v1 [cs.DS] 13 Jul 2024 Page 1 MIOV: Reordering MOVI for even better
locality Peter Perešıni1, Nathaniel K. Brown2, Travis Gagie3, and Ben Langmead2 1 …
locality Peter Perešıni1, Nathaniel K. Brown2, Travis Gagie3, and Ben Langmead2 1 …
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data
As next-generation sequencing technologies produce deeper genome coverages at lower
costs, there is a critical need for reliable computational host DNA removal in metagenomic …
costs, there is a critical need for reliable computational host DNA removal in metagenomic …
Developing compressed linear pangenome indexes for rapid sequence classification
O Ahmed - 2024 - jscholarship.library.jhu.edu
A reference genome serves an important function for various genomic analyses; it acts as a
template to be used to match sequencing reads to the genome and provides a coordinate …
template to be used to match sequencing reads to the genome and provides a coordinate …