Matching Reads to Many Genomes with the r -Index
Copyright policy )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 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 .
- JOHNS HOPKINS UNIVERSITY
- Johns Hopkins University United States
- University of Florida
- Dalhousie University Canada
- University of Florida United States
Genomics (q-bio.GN), FOS: Computer and information sciences, Genome, Genomics, Sequence Analysis, DNA, 004, Burrows-Wheeler Transform; indexing; pan-genomics; r-index, r-index, FOS: Biological sciences, Computer Science - Data Structures and Algorithms, Databases, Genetic, Humans, Quantitative Biology - Genomics, Data Structures and Algorithms (cs.DS), Burrows-Wheeler Transform, pan-genomic, Sequence Alignment, Research Articles, Software, indexing
Genomics (q-bio.GN), FOS: Computer and information sciences, Genome, Genomics, Sequence Analysis, DNA, 004, Burrows-Wheeler Transform; indexing; pan-genomics; r-index, r-index, FOS: Biological sciences, Computer Science - Data Structures and Algorithms, Databases, Genetic, Humans, Quantitative Biology - Genomics, Data Structures and Algorithms (cs.DS), Burrows-Wheeler Transform, pan-genomic, Sequence Alignment, Research Articles, Software, indexing
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