Matching Reads to Many Genomes with the r-Index

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...

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Detalles Bibliográficos
Autores principales: Mun, Taher, Kuhnle, Alan, Boucher, Christina, Gagie, Travis, Langmead, Ben, Manzini, Giovanni
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Mary Ann Liebert, Inc., publishers 2020
Materias:
Research Articles
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7185317/
https://www.ncbi.nlm.nih.gov/pubmed/32181686
http://dx.doi.org/10.1089/cmb.2019.0316
Descripción
Sumario: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.

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