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arXiv · 1908.01263

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

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

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Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini. 2019-08-04. Matching reads to many genomes with the $r$-index. https://arxiv.org/abs/1908.01263

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