This project has the overall goal of identifying, quantifying, and verifying the presence of microbes and viruses in the Tijuana River Basin.
Sample data is available through the European Nucleotide Archive Project: PRJEB57859 and Run Accessions are available in the mapping files. An R Markdown or Jupyter Notebook is supplied to run code or scripts in the correct order.
Theoretically, anyone should be able to input their data into the correct data folder and replicate my results as long as the files are labeled as described.
fastp_Kaiju_processing takes paired-end metagenomic sequencing reads, with R1 and R2 identifying read direction, quality controls, taxonomically classifies using Kaiju, creates OTU tables and modifies those OTU tables for use in R for analysis. Input is fastq.gz, output is kaiju .out files, kaiju .tsv files, OTU tables, and a final metagenomemodified.csv file that can be used with an associated mapping file for analysis in R.
Diversity_Analysis takes metagenomic data and a mapping file as input, performs a centered log-ratio (clr) transformation, and outputs a NMDS Plot and performs statistical analysis on the beta-diversity of the samples.
Fecal_Contamination takes metagenomic data and isolates crAssphage, a phage commonly associated with human fecal contamination, and HF183 bacteria, which are associated with the HF183 PCR Primer used to measure fecal contamination levels, and uses them as inputs. The two associated factors then undergo statistical analysis and a regression is plotted grouped by location and date.