RT Journal
A1 Fiddes, Ian T.
A1 Armstrong, Joel
A1 Diekhans, Mark
A1 Nachtweide, Stefanie
A1 Kronenberg, Zev N.
A1 Underwood, Jason G.
A1 Gordon, David
A1 Earl, Dent
A1 Keane, Thomas
A1 Eichler, Evan E.
A1 Haussler, David
A1 Stanke, Mario
A1 Paten, Benedict
T1 Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
JF Genome Research 
JO Genome Research 
YR 2018 
FD July 01 
VO 28 
IS 7 
SP 1029 
OP 1038 
DO 10.1101/gr.233460.117 
UL http://genome.cshlp.org/content/28/7/1029.abstract 
AB The recent introductions of low-cost, long-read, and read-cloud sequencing technologies coupled with intense efforts to develop efficient algorithms have made affordable, high-quality de novo sequence assembly a realistic proposition. The result is an explosion of new, ultracontiguous genome assemblies. To compare these genomes, we need robust methods for genome annotation. We describe the fully open source Comparative Annotation Toolkit (CAT), which provides a flexible way to simultaneously annotate entire clades and identify orthology relationships. We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. We demonstrate the resulting discovery of novel genes, isoforms, and structural variants—even in genomes as well studied as rat and the great apes—and how these annotations improve cross-species RNA expression experiments.