Playing around with graphs for the DNA code club.
- 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
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;
git clone https://github.com/vgteam/vg.git
- use the following command to run the bash script:
bash run_vg.sh
- Check out the following guide on using the vg tiny example vg tiny example