Code packages and apps to conduct efficient analyses on genetics and evolution
TIGER integrates a collection of toolkits facilitating research analyses on genetics and evolution. It is a Java-based program, combining efficiency and flexibility to realize high-performance computation of various types of analysis.
TIGER is designed to simplify its usage for the convenience of end users. It has integrated a list of applications (Apps). Users can run apps in TIGER by selecting an app and specify its parameters. TIGER has two sets of options. There is only one option in the first set, which is "-app" and is used to select an app. The other set of options is app-specific parameters, which are listed using alphabet letters in most cases. Below is how app options look like in TIGER.
- -app, the name of the selected app
- -a, parameter_a
- -b, parameter_b
- ...
Take running app FastCall as an example, the command line is,
- java -Xmx100g -jar TIGER.jar -app FastCall -a chr001.fa -b taxaBamMap.txt -c 30 -d 20 -e 2 -f 0.2 -g 3 -h 0.8 -i 0.4 -j 0.2 -k 1 -l 32 -m /ing -n /usr/local/bin/samtools > log.txt &
TIGER will be developed in a long-term basis. Detailed usage of apps can be seen below.
- 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.
- 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