ilus 0.1.0

ilus: A WGS/WES analysis pipeline generater.

Ilus is a handy NGS pipeline for whole genome re-sequencing (WGS) data analysis.

Installation

Ilus is writed by Python and maintain in PyPI. You can install it just by running the following command:

pip install ilus

You can type ilus in your commandline terminal if everything is smooth.

Quick Start

There are several functions in ilus:

$ ilus --help

You will see all the functions:

usage: ilus [-h] {WGS,genotype-joint-calling,VQSR} ...

ilus: A WGS analysis pipeline.

optional arguments:
    -h, --help            show this help message and exit

ilus commands:
{WGS,genotype-joint-calling,VQSR}
    WGS                 Creating pipeline for WGS(from fastq to genotype VCF)
    genotype-joint-calling Genotype from GVCFs.
    VQSR                VQSR

Run GATK Best Practices Workflow

ilus implelement the whole WGS analysis workflow base on the [GATK Best Practices](https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows).