no code implementations • 29 Jan 2021 • Travis Gagie
Let $G$ be a Wheeler graph and $r$ be the number of runs in a Burrows-Wheeler Transform of $G$, and suppose $G$ can be decomposed into $\upsilon$ edge-disjoint directed paths whose internal vertices each have in- and out-degree exactly 1.
Data Structures and Algorithms
no code implementations • 19 Sep 2018 • Travis Gagie, Garance Gourdel, Giovanni Manzini
Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting onto it the reads that align to it, at the starting positions of their alignments.
Data Structures and Algorithms Genomics
1 code implementation • 24 May 2017 • Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Here we extend the approach so that one of the inputs can be a directed acyclic graph (DAGs), e. g. a splicing graph in transcriptomics or a variant graph in pan-genomics.
Data Structures and Algorithms G.2.2; F.2.2; J.3
1 code implementation • 27 Mar 2009 • Travis Gagie, Simon J. Puglisi, Andrew Turpin
A range quantile query takes a rank and the endpoints of a sublist and returns the number with that rank in that sublist.
Data Structures and Algorithms
