ww_simulations

A series of scripts to generate simulated datasets of different variant composition for SC2 wastewater surveillance efforts.

Dependencies

• python (3.8.1)
• art
• in_silico_pcr.pl

Usage

• generate_replicates.py can be used to create replicate datasets each with a random composition of a fixed number of variants

Example: generate_replicates.py -i accessions.txt -n 2 -o test_output

• generate_simulated_datasets.py takes the ouput of generate_replicates.py and a number of other files/arguments and generates simulated data reflecting the composition of the variants

Example: generate_simulated_datasets.py -f five_sequences.fasta -i test_output_replicate_1.tsv -p neb_vss1a_primer.tsv -n 10

Workflow/strategy

• generate_simulated_datasets.py models differences in variation composition by multiplying the number of each amplicon from each variant by the percent abundance it is in the simulated 'sample'.
• The total reads of is determined by the -f flag passed to art which is "the fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon"