Matching Reads to Many Genomes with the r -Index
Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini · Journal of Computational Biology · 2020
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.