1 citations · 1 across the 5 of their papers we have counts for
5 papers · 1 filter
Patching leaky tunnels in BWTs
Paola Bonizzoni, Davide Cozzi, Travis Gagie +2
We extend Baier's foundationial work on tunnelling Burrows-Wheeler Transforms (BWTs) by showing how something that would be a good tunnel except for a strings that diverge from the…
Faster Iterative Queries on the Positional BWT
Paola Bonizzoni, Travis Gagie, Younan Gao
The Positional Burrows-Wheeler Transform (PBWT) is a fundamental data structure for the efficient representation and analysis of large-scale haplotype panels. For a panel of se…
KeBaB: -mer based breaking for finding long MEMs
Nathaniel K. Brown, Lore Depuydt, Mohsen Zakeri +8
Long maximal exact matches (MEMs) are used in many genomics applications such as read classification and sequence alignment. Li's ropebwt3 finds long MEMs quickly because it can of…
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.
Maximal Unbordered Factors of Random Strings
Patrick Hagge Cording, Travis Gagie, Mathias Bæk Tejs Knudsen +1
A border of a string is a non-empty prefix of the string that is also a suffix of the string, and a string is unbordered if it has no border other than itself. Loptev, Kucherov, an…