OIL-PCR_Linking_plasmid-based_beta-lactamases

For OIL-PCR:

1. Use script examples in "merge_split_filter" to process the raw reads into target and 16S portions
2. QC scripts will compile read counts at each step of processing
3. Use scripts in "cluster_assign_tax" to assign taxonomy to the 16S portions
4. Use scripts in "blast" to identify the target portion
5. Use jupyter book in "compile_all_data" to compile blast and taxonomy data along with read counts into the final data table

16S sequencing

Scripts for processing the 16S data and preparing rarefaction curves are in "16S_and_rarefaction"