The full readme will be available soon
This rebalances multiplex primer schemes as described in "Improving the evenness of SARS-CoV-2 genome coverage by titration of primer concentration"
To install
git clone https://github.com/ChrisgKent/primer_rebalance_SM
Activate/install the conda environment
cd primer_rebalance
conda env create -f primer_rebalance.yaml
conda activate primer_rebalance
--config scheme=<file_to_scheme.bed> mapped_bed_dir=<dir> output_dir=results/
scheme - Should provide a path to a .bed file, containing the locations of the primers used in the scheme. In the same format as PrimalScheme generates (ref, start, end, name, pool, strand, sequence)
mapped_bed_dir - Point to a directory containing only the mapped .bam files. Such a the .sorted.bam files from ncov-artic-nf pipeline
output_dir - The output directory, containing the results. Defaults to results
total_pool_ul - The total volume of each 100mM pool in ul. Defaults to 500