2 citations · 2 across the 7 of their papers we have counts for
9 papers · 1 filter
Optimal-Time Move Structure Construction
Nathaniel K. Brown, Ahsan Sanaullah, Shaojie Zhang +1
The move structure represents a permutation of by partitioning the domain into disjoint, contiguously permuted intervals, with being the minimum number of su…
MIOV: Reordering MOVI for even better locality
Peter Perešíni, Nathaniel K. Brown, Travis Gagie +1
We consider how to reorder the rows of Nishimoto and Tabei's move structure such that we more often move from one row to the next in memory.
Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests
Dominika Draesslerová, Omar Ahmed, Travis Gagie +4
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain th…
Suffixient Sets
Lore Depuydt, Travis Gagie, Ben Langmead +2
We define a suffixient set for a text to be a set of positions between 1 and such that, for any edge descending from a node to a node in the suffix tree…
KATKA: A KRAKEN-like tool with given at query time
Travis Gagie, Sana Kashgouli, Ben Langmead
We describe a new tool, KATKA, that stores a phylogenetic tree such that later, given a pattern and an integer , it can quickly return the root of the smallest su…
PHONI: Streamed Matching Statistics with Multi-Genome References
Christina Boucher, Travis Gagie, Tomohiro I +6
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic data…
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…
Prefix-Free Parsing for Building Big BWTs
Christina Boucher, Travis Gagie, Alan Kuhnle +3
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to buil…