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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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
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author Mun, Taher
Kuhnle, Alan
Boucher, Christina
Gagie, Travis
Langmead, Ben
Manzini, Giovanni
author_facet Mun, Taher
Kuhnle, Alan
Boucher, Christina
Gagie, Travis
Langmead, Ben
Manzini, Giovanni
author_sort Mun, Taher
collection PubMed
description 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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spelling pubmed-71853172020-05-06 Matching Reads to Many Genomes with the r-Index Mun, Taher Kuhnle, Alan Boucher, Christina Gagie, Travis Langmead, Ben Manzini, Giovanni J Comput Biol Research Articles 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. Mary Ann Liebert, Inc., publishers 2020-04-01 2020-04-08 /pmc/articles/PMC7185317/ /pubmed/32181686 http://dx.doi.org/10.1089/cmb.2019.0316 Text en © Taher Mun, et al., 2020. Published by Mary Ann Liebert, Inc. This Open Access article is distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research Articles
Mun, Taher
Kuhnle, Alan
Boucher, Christina
Gagie, Travis
Langmead, Ben
Manzini, Giovanni
Matching Reads to Many Genomes with the r-Index
title Matching Reads to Many Genomes with the r-Index
title_full Matching Reads to Many Genomes with the r-Index
title_fullStr Matching Reads to Many Genomes with the r-Index
title_full_unstemmed Matching Reads to Many Genomes with the r-Index
title_short Matching Reads to Many Genomes with the r-Index
title_sort matching reads to many genomes with the r-index
topic Research Articles
url 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
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