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graphplay's Introduction

graphPlay

Playing around with graphs for the DNA code club.

Before anything, install the following:

  • use the following through conda:
conda install -c bioconda vg

  • install bandage for visualizing graph genomes: Bandage Wesbite

  • install the AWS CLI

conda install -c conda-forge awscli

HISAT

aws s3 cp s3://genome-idx/bt/grch38_1kgmaj.zip .

export PATH=hisat-genotype-top:hisat-genotype-top/hisatgenotype_scripts:$PATH;
export PYTHONPATH=hisat-genotype-top/hisatgenotype_modules:$PYTHONPATH;

OR

echo "export PATH=hisat-genotype-top:hisat-genotype-top/hisatgenotype_scripts:$PATH;" >> ~/.bashrc;
echo "export PYTHONPATH=hisat-genotype-top/hisatgenotype_modules:$PYTHONPATH;" >> ~/.bashrc;
source ~/.bashrc;

download the vg git repo, for examples

git clone https://github.com/vgteam/vg.git

Usage

  • use the following command to run the bash script:
bash run_vg.sh

Next

  • Check out the following guide on using the vg tiny example vg tiny example

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