Toolkits Integrated for Genetic and Evolutionary Research
Code packages and apps to conduct efficient genetic and evolutionary analysis
Overview
TIGER integrates a collection of toolkits facilitating research analysis on genetics and evolution. It is a Java based program, combining efficiency and flexibility to realize high-performance computation of various types of analysis.
Usage
TIGER is designed to simpliy its usage for the convinience of end users. It has a list of applications (Apps). Each app has a parameter file, where app parameters can be specified in the parameter file. Users can run apps in TIGER by selecting an app and specifify its parameters. TIGER has only two options,
- -a, the name of the selected app
- -p, the path of the parameter file
Take running app FastCall as an example, the commnand line is,
- java -Xmx100g -jar TIGER.jar -a FastCall -p ./parameter_fastcall.txt > log.txt &
TIGER will be developed in a long-term basis. Detailed usage of apps can be seen below.
User Manual of Apps
- FastCall -Superfast variant calling and genotyping for whole-genome shotgun (WGS) sequencing data.
- HapScanner-Superfast genotyper for whole-genome shotgun (WGS) sequencing data, based on an existing genetic variation library.
- PopDep-Read depth profiler for a population, based on whole-genome shotgun (WGS) sequencing data..
Developer Manual
Releases
Citations
- FastCall
Punna Ramu, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu. (2017). Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. doi: 10.1038/ng.3845! - HapScanner
Y. Zhou, X. Zhao, Y. Li, J. Xu, A. Bi, L. Kang, D. Xu, H. Chen, Y. Wang, Y. Wang, S. Liu, C. Jiao, H. Lu, J. Wang, C. Yin, Y. Jiao, F. Lu. (2020). Triticum population sequencing provides insights into wheat adaptation. Nature Genetics. doi:10.1038/s41588-020-00722-w