convex-qsr

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

Install

Available via conda from the stephenshank channel (coming soon to bioconda):

conda config --add channels stephenshank
conda install convex-qsr

Also available via pip and the PyPI:

pip install convex-qsr

Run

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

Test

python -m unittest discover