PT  - JOURNAL ARTICLE
AU  - Tao Zhu
AU  - Chengzhen Liang
AU  - Zhigang Meng
AU  - Sandui Guo
AU  - Rui Zhang
TI  - GFF3sort: an efficient tool to sort GFF3 files for tabix indexing
AID  - 10.1101/145938
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 145938
4099  - http://biorxiv.org/content/early/2017/06/29/145938.short
4100  - http://biorxiv.org/content/early/2017/06/29/145938.full
AB  - Background 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, either by remembering their original orders or by conducting parent-child topology sorting. Based on our test datasets from seven species, GFF3sort produced accurate sorting results while taking significantly less running time compared with currently available tools.Conclusions GFF3sort is an efficient tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be a useful tool to help with genome annotation data processing and visualization.JBrowseJavaScript-based genome browserGFF3General Feature Format, version 3JSONJavaScript Object NotationHTML5HyperText Markup Language, version 5