Matching Reads to Many Genomes with the r-Index

Taher Mun; Alan Kuhnle; Christina Boucher; Travis Gagie; Ben Langmead; Giovanni Manzini

doi:10.1089/cmb.2019.0316

Matching Reads to Many Genomes with the r-Index

J Comput Biol. 2020 Apr;27(4):514-518. doi: 10.1089/cmb.2019.0316. Epub 2020 Mar 16.

Authors

Taher Mun¹, Alan Kuhnle², Christina Boucher², Travis Gagie³, Ben Langmead¹, Giovanni Manzini⁴

Affiliations

¹ Department of Computer Science, Johns Hopkins University, Baltimore, Maryland.
² Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida.
³ Faculty of Computer Science, Dalhousie University, Halifax, Canada Center for Biotechnology and Bioengineering, Santiago, Chile School of Computer Science and Telecommunications, Universidad Diego Portales, Santiago, Chile.
⁴ Department of Science and Technological Innovation, University of Eastern Piedmont, Alessandria, Italy.

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.

Keywords: Burrows–Wheeler Transform; indexing; pan-genomics; r-index.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Databases, Genetic
Genome / genetics*
Genomics*
Humans
Sequence Alignment / methods
Sequence Analysis, DNA / methods*
Software

Abstract

Publication types

MeSH terms

Grants and funding