# Matching reads to many genomes with the $r$-index

## TL;DR

This paper introduces methods for constructing and querying the $r$-index, a compressed genomic database index, enabling efficient exact read matching and seed finding for genomic sequences.

## Contribution

It provides practical tools and procedures for building and using the $r$-index with real genomic data, facilitating efficient read alignment.

## Key findings

- Efficient construction of $r$-index from FASTA files
- Effective querying of $r$-index for exact pattern matching
- Open-source implementation available under GPLv3

## 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 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 $r$-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 .