RT Journal Article
SR Electronic
T1 A Flow Procedure for the Linearization of Genome Sequence Graphs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 101501
DO 10.1101/101501
A1 David Haussler
A1 Maciej Smuga-Otto
A1 Benedict Paten
A1 Adam M Novak
A1 Sergei Nikitin
A1 Maria Zueva
A1 Dmitrii Miagkov
YR 2017
UL http://biorxiv.org/content/early/2017/01/18/101501.abstract
AB Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within a species, a genome sequence graph. A sequence graph represents a set of individual haploid reference genomes as paths in a single graph. When that set of reference genomes is sufficiently diverse, the sequence graph implicitly contains all frequent human genetic variations, including translocations, inversions, deletions, and insertions.In representing a set of genomes as a sequence graph one encounters certain challenges. One of the most important is the problem of graph linearization, essential both for efficiency of storage and access, as well as for natural graph visualization and compatibility with other tools. The goal of graph linearization is to order nodes of the graph in such a way that operations such as access, traversal and visualization are as efficient and effective as possible.A new algorithm for the linearization of sequence graphs, called the flow procedure, is proposed in this paper. Comparative experimental evaluation of the flow procedure against other algorithms shows that it outperforms its rivals in the metrics most relevant to sequence graphs.