3 papers
cs.DS2018
Haplotype-aware graph indexes
Jouni Sirén, Erik Garrison, Adam M. Novak +2
The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true hap…
cs.DS2016
RLZAP: Relative Lempel-Ziv with Adaptive Pointers
Anthony J. Cox, Andrea Farruggia, Travis Gagie +2
Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s…
cs.DS2015
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…