RT Journal Article
SR Electronic
T1 GFF3sort: an efficient tool to sort GFF3 files for tabix indexing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 145938
DO 10.1101/145938
A1 Tao Zhu
A1 Chengzhen Liang
A1 Zhigang Meng
A1 Sandui Guo
A1 Rui Zhang
YR 2017
UL http://biorxiv.org/content/early/2017/06/04/145938.abstract
AB Motivation The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have bugs that would lead to erroneous rendering in JBrowse.Results We developed GFF3sort, a script to sort GFF3 files for tabix indexing. GFF3sort can properly deal with the order of features that have the same chromosome and start position. Based on our test datasets from multiple species, GFF3sort produced accurate sorting results while taking significantly less running time compared with currently available tools. We anticipate that GFF3sort will be a useful tool to help with genome annotation data processing and visualization.Availability https://github.com/billzt/gff3sort