Work

Matching Reads to Many Genomes with the r -Index

Year: 2020

Type: article

Abstract: The r -index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a genome in the database or to find seeds for reads that do not. This article shows how to download and install the programs ri-buildfasta and ri-align; how to call ri-buildfasta on an FASTA file to build an r -index for that file; and how to query that index with ri-align.

Source: Journal of Computational Biology

DOI: 10.1089/cmb.2019.0316

Authors: Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini

Institutions: Johns Hopkins University, University of Florida, Dalhousie University, Centre for Biotechnology and Bioengineering, Universidad Diego Portales, Università degli Studi del Piemonte Orientale “Amedeo Avogadro”

Language: English

Topic: Algorithms and Data Compression

Subfield: Artificial Intelligence

Field: Computer Science

Domain: Physical Sciences

Open Access status: hybrid

Funders: National Science Foundation, Istituto Nazionale di Alta Matematica "Francesco Severi", Dalhousie University, National Institutes of Health, Gruppo Nazionale per il Calcolo Scientifico, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases

Awards: III: Small: Collaborative Research: A Scalable and Efficient Optical Map Assembler, CAREER: BCSP: Methods for analyzing sequencing data from repetitive genomes, Developing Computational Methods for Surveillance of Antimicrobial Resistant Agents, Hardening and Scaling Core Genomics Software

OpenAlex ID: W3011828211

FWCI: 0.589

Cites: 10

Cited by: 10

Related to: 10