• reference genome sequence (.fa)
• sequenced viral genomes representing genetic diversity (.fa)
• Cas13a repeat sequence

• bowtie
• RNAfold
• R, with libraries: optparse, here, Biostrings, parallel, doParallel

Documentation

1. Break reference genome into windows of 20nt: break_genome.R

• need reference genome .fa file

1. Score window sensitivity to SARS-CoV-2: score_SARS-CoV-2_sensitivity.R

• need .fa file of sequenced viral genomes representing genetic diversity

1. Score specificity against other human coronaviruses: score_human_CoV_specificity.R

• need .fa file of offtarget coronavirus genomes

1. Calculate crRNA folding structures (RNAfold): score_RNAfold_crRNAs.R

2. Calculate base-pairing propensity of viral target window: score_RNAfold_target.R

3. Align against hg38 transcriptome: align_bowtie.R

4. Align against bosTau9 transcriptome: align_bowtie.R

5. Compile scores into aggregate summary table: compile_scores.R

sample processing script: outputs/covid/cas13a_20nt/process.sh