/TIGER

Toolkits Integrated for Genetic and Evolutionary Research

Primary LanguageJavaGNU General Public License v3.0GPL-3.0

Toolkits Integrated for Genetic and Evolutionary Research

Code packages and apps to conduct efficient analyses on genetics and evolution

Overview

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.

Usage

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.

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