Revision 6d5b25dfa6d67703f06f74c24f7efe27bcf9d8dd authored by pjdiebold on 15 June 2021, 20:27:54 UTC, committed by GitHub on 15 June 2021, 20:27:54 UTC
1 parent 54a69fb
README.md
# 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"
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