TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining

Chengjie Chen; Ya Wu; Jiawei Li; Xiao Wang; Zaohai Zeng; Jing Xu; Yuanlong Liu; Junting Feng; Hao Chen; Yehua He; Rui Xia

doi:10.1016/j.molp.2023.09.010

TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining

Mol Plant. 2023 Nov 6;16(11):1733-1742. doi: 10.1016/j.molp.2023.09.010. Epub 2023 Sep 22.

Authors

Chengjie Chen¹, Ya Wu², Jiawei Li³, Xiao Wang⁴, Zaohai Zeng⁵, Jing Xu⁵, Yuanlong Liu⁵, Junting Feng⁶, Hao Chen⁷, Yehua He², Rui Xia⁸

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China. Electronic address: ccj@scau.edu.cn.
² State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China.
³ Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong 510632, China.
⁴ State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng 475004, China.
⁵ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China.
⁶ Key Laboratory of Genetic Improvement of Bananas, Sanya Research Institute, State Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
⁷ College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
⁸ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China. Electronic address: rxia@scau.edu.cn.

PMID: 37740491
DOI: 10.1016/j.molp.2023.09.010

Abstract

Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles. Now, TBtools is a commonly used tool in biological laboratories. Over the past 3 years, thanks to invaluable feedback and suggestions from numerous users, we have optimized and expanded the functionality of the toolkit, leading to the development of an upgraded version-TBtools-II. In this upgrade, we have incorporated over 100 new features, such as those for comparative genomics analysis, phylogenetic analysis, and data visualization. Meanwhile, to better meet the increasing needs of personalized data analysis, we have launched the plugin mode, which enables users to develop their own plugins and manage their selection, installation, and removal according to individual needs. To date, the plugin store has amassed over 50 plugins, with more than half of them being independently developed and contributed by TBtools users. These plugins offer a range of data analysis options including co-expression network analysis, single-cell data analysis, and bulked segregant analysis sequencing data analysis. Overall, TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors. By promoting the theme "one for all, all for one", we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.

Keywords: BSA-seq; TBtools-II; biological big data; plugin.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Big Data
Computational Biology*
Data Mining
Phylogeny
Software*