GFF3sort: a novel tool to sort GFF3 files for tabix indexing
Abstract 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...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2017-11-01
|
Series: | BMC Bioinformatics |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12859-017-1930-3 |
id |
doaj-82e6738e64ad4ed5a28ef060cbe134f4 |
---|---|
record_format |
Article |
spelling |
doaj-82e6738e64ad4ed5a28ef060cbe134f42020-11-24T21:39:12ZengBMCBMC Bioinformatics1471-21052017-11-011811410.1186/s12859-017-1930-3GFF3sort: a novel tool to sort GFF3 files for tabix indexingTao Zhu0Chengzhen Liang1Zhigang Meng2Sandui Guo3Rui Zhang4Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesBiotechnology Research Institute, Chinese Academy of Agricultural SciencesAbstract 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 some limitations and their sorting results would lead to erroneous rendering in JBrowse. Results We developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, 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 with acceptable efficiency compared with currently available tools. Conclusions GFF3sort is a novel tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be useful to help with genome annotation data processing and visualization.http://link.springer.com/article/10.1186/s12859-017-1930-3GFF3JBrowseVisualizationTabix |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Tao Zhu Chengzhen Liang Zhigang Meng Sandui Guo Rui Zhang |
spellingShingle |
Tao Zhu Chengzhen Liang Zhigang Meng Sandui Guo Rui Zhang GFF3sort: a novel tool to sort GFF3 files for tabix indexing BMC Bioinformatics GFF3 JBrowse Visualization Tabix |
author_facet |
Tao Zhu Chengzhen Liang Zhigang Meng Sandui Guo Rui Zhang |
author_sort |
Tao Zhu |
title |
GFF3sort: a novel tool to sort GFF3 files for tabix indexing |
title_short |
GFF3sort: a novel tool to sort GFF3 files for tabix indexing |
title_full |
GFF3sort: a novel tool to sort GFF3 files for tabix indexing |
title_fullStr |
GFF3sort: a novel tool to sort GFF3 files for tabix indexing |
title_full_unstemmed |
GFF3sort: a novel tool to sort GFF3 files for tabix indexing |
title_sort |
gff3sort: a novel tool to sort gff3 files for tabix indexing |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2017-11-01 |
description |
Abstract 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 some limitations and their sorting results would lead to erroneous rendering in JBrowse. Results We developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, 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 with acceptable efficiency compared with currently available tools. Conclusions GFF3sort is a novel tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be useful to help with genome annotation data processing and visualization. |
topic |
GFF3 JBrowse Visualization Tabix |
url |
http://link.springer.com/article/10.1186/s12859-017-1930-3 |
work_keys_str_mv |
AT taozhu gff3sortanoveltooltosortgff3filesfortabixindexing AT chengzhenliang gff3sortanoveltooltosortgff3filesfortabixindexing AT zhigangmeng gff3sortanoveltooltosortgff3filesfortabixindexing AT sanduiguo gff3sortanoveltooltosortgff3filesfortabixindexing AT ruizhang gff3sortanoveltooltosortgff3filesfortabixindexing |
_version_ |
1725931955869974528 |