Matching reads to many genomes with the $r$-index
Data Structures and Algorithms
2019-08-06 v1 Genomics
Abstract
The -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 paper shows how to download and install the programs ri-buildfasta and ri-align; how to call ri-buildfasta on a FASTA file to build an -index for that file; and how to query that index with ri-align. Availability: The source code for these programs is released under GPLv3 and available at https://github.com/alshai/r-index .
Keywords
Cite
@article{arxiv.1908.01263,
title = {Matching reads to many genomes with the $r$-index},
author = {Taher Mun and Alan Kuhnle and Christina Boucher and Travis Gagie and Ben Langmead and Giovanni Manzini},
journal= {arXiv preprint arXiv:1908.01263},
year = {2019}
}