RT Journal
A1 Paten, Benedict
A1 Novak, Adam M.
A1 Eizenga, Jordan M.
A1 Garrison, Erik
T1 Genome graphs and the evolution of genome inference
JF Genome Research 
JO Genome Research 
YR 2017 
FD May 01 
VO 27 
IS 5 
SP 665 
OP 676 
DO 10.1101/gr.214155.116 
UL http://genome.cshlp.org/content/27/5/665.abstract 
AB The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph-based models. Here, we survey various projects underway to build and apply these graph-based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce.