mariaelf97/simulate_reads

Simulating amplicon sequencing reads

Amplicon read simulation for waste water

Steps to simulate reads

There are two methods for amplicon extraction using bed-formatted primer file.

1. Alignment approach: This method use bowtie2 as an aligner to map the primers to a provided whole genome fasta file. The default parameters for an end to end alignment are used. src/create_amplicons/alignment_based

2. Basic string match approach: This approach uses a strict pattern matching approach allowing up to 3 mismatches. This method does not take indels into account. src/create_amplicons/pattern_match

Once the amplicons are created, wgsim is used as a short-read simulator to simulate amplicon reads. src/variant_calling src/read_simulation