4 papers
PFP Data Structures
Christina Boucher, Ondřej Cvacho, Travis Gagie +4
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a…
Matching reads to many genomes with the -index
Taher Mun, Alan Kuhnle, Christina Boucher +3
The -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 gen…
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
Alan Kuhnle, Taher Mun, Christina Boucher +3
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousa…
Relative Select
Christina Boucher, Alexander Bowe, Travis Gagie +2
Motivated by the problem of storing coloured de Bruijn graphs, we show how, if we can already support fast select queries on one string, then we can store a little extra informatio…