davebx/convex-qsr

Viral quasispecies reconstruction using convex optimization

convex-qsr

Reference-guided viral quasispecies reconstruction using convex optimization. Under development.

Install

git clone https://github.com/stephenshank/convex-qsr
cd convex-qsr
python setup.py install

pip and conda installable packages coming soon.

Run

cqsr_ec -b sorted.bam -o output
cqsr_rg -i output -o output
cqsr_qr -i output -o output
cqsr_viz -o output

Test

python -m unittest discover