GRAde

A GRA detection pipeline

Clone GRAde via Git Large File Storage (LFS)

Install Git Large File Storage: https://git-lfs.github.com/

sudo apt-get install git-lfs 
# or install with conda
conda install -c conda-forge git-lfs

Clone this repository

git clone https://github.com/hsu-binfo/GRAde.git

If you have miniconda or anaconda installed, you can skip this step.
Install miniconda: https://conda.io/projects/conda/en/latest/user-guide/install/index.html

Install GRAde dependencies with the following command

cd GRAde
conda env create -n GRAde --file environment.yml
conda activate GRAde

Done!

python GRAdetection.py

python GRAdetection.py --fastq example/example1.fastq.gz --outdir /path/to/output/dir/ --samplename GRAtesting

July 2020

Name		Name	Last commit message	Last commit date
Latest commit History 61 Commits
db		db
example		example
scripts		scripts
.gitattributes		.gitattributes
GRAde.py		GRAde.py
README.md		README.md
align_spectrum.py		align_spectrum.py
basecalling.py		basecalling.py
config.json		config.json
environment.yml		environment.yml
findOverlap.py		findOverlap.py
parse_diff_sites.py		parse_diff_sites.py
pattern_align_4k.py		pattern_align_4k.py
sam2fasta.py		sam2fasta.py
typing_plot.R		typing_plot.R