Saw Kill river (NY, USA) metagenomics and environmental variables

Original raw sequences are available in NCBI SRA (Accession: PRJNA565393)
Sample sites and sample names are in "Sawkill_mapping_and_env_var.csv"
All scripts used are located in "Combined_Scripts.rmd".

This dataset includes the following files:

• Sampling_site_metadata_table.csv - Sample ID, Field ID, Date, Cumulative Rain Fall (mm), and Air Temperature (°C)
• Physicochemical_characteristics.csv - Sample ID, Water Temperature (ºC), Turbidity (TU), Conductivity (µmhos/cm), Dissolved Oxygen (mgL), and Salinity (ppt)
• Escherichia_coli_concentration.csv - Sample ID, E. coli (MPN·100mL-1)
• Total_coliforms_concentration.csv - Sample ID, Coliform (MPN·100mL-1)
• Enterococcus_sp_concentration.csv - Sample ID, Enterococcus sp. (MPN·100mL-1)
• Endotoxins_concentation.csv - Sample ID, Endotoxin (EU/mL)
• Integron_1_relative_abundance.csv - Sample ID, intI1 rel. abun.
• ASV_and_taxa_assignment.tsv - Tab separated file with each ASV, assigned taxa, and percent confidence (aka, ASV_to_taxa_confidece.tsv)
• Taxa_abundance_by_sample.csv - All taxa at species level resolution (or lowest possible) and abundances in each sample (aka, Species_resolved_taxa_and_counts.csv)
• Sawkill_mapping_and_env_var.csv - comma-separated file containing sample names and sample sites and measured environmental variables.
  • detail: SampleID - Unique Identifier: SK-<sort_number>   
  • sort - Unique Identifier index number
  • FieldID - Combination field: <site>_<date> combination of site column and date column
  • Date - Calendar date
  • Day - Sample index starting at one (06/22/2015) and incrementing by one for each additional sample date
  • Site - Location of Sample site and Replicate number (Counting from 0):
  • OW = Outflow Water
  • AS# = Above Outflow Sediment (Far) (NB: AS = replicate 0, AS1 = replicate 1)
  • A1S# = Above Outflow Sediment (Near) (NB: A1S = replicate 0, A1S1 = replicate 1)
  • BS# = Below Outflow Sediment (Near) (NB: BS = replicate 0, BS1 = replicate 1)
  • B1S# = Below Outflow Sediment (Far) (NB: B1S = replicate 0, B1S1 = replicate 1)
  • AW = Above Outflow Sediment (Far)
  • A1W = Above Outflow Sediment (Near)
  • BW = Below Outflow Sediment (Near)
  • B1W = Below Outflow Sediment (Far)
  • GeoLocation - Spatial location of sample site
  • O = Outflow
  • A = Above Outflow (Far)
  • A1 = Above Outflow (Near)
  • B = Below Outflow (Near)
  • B1 = Below Outflow (Far)
  • Type - Physical matrix sampled (Outflow, Sediment, Water)
  • Desc - Brief text description of Sample
  • Pool - Brief text description of Sample Group
  • Rain12 - Cumulative Measure of Rain (mm) collected over the previous 12 hours.   
  • Rain24 - Cumulative Measure of Rain (mm) collected over the previous 24 hours.   
  • Rain48 - Cumulative Measure of Rain (mm) collected over the previous 48 hours.   
  • Rain72 - Cumulative Measure of Rain (mm) collected over the previous 72 hours.
  • AirTemp - Ambient air temperture (Celsius)
  • WaterTemp - Temperature of water at collection site (Celsius)
  • Turbidity - Water Turbidity (TU)
  • Conductivity - Water Conductivity (µmhos/cm)
  • DO_mgl - Water Dissolved Oxygen (mgL)
  • salinity_ppt - Water Salinity (ppt)
  • intI1 - Relative abundance of intI1 using qPCR
  • Ecoli - IDEXX Colilert assay (MPN·100mL-1)
  • Coliform - IDEXX Colilert assay (MPN·100mL-1)
  • Entero - IDEXX Enterolert (MPN·100mL-1)
  • Endotoxins - Charles River Endosafe system (EU/mL)
• Denoising_qc_stats.tsv - tab separated file with the following read abundances per sample 'input', filtered', 'denoised', 'merged', and 'non-chimeric'.
• Sample_frequency_detail.csv - Reads used per sample
• Sample_site_GPS.txt - Map refined estimated GPS coordinates (decimal format) of all sample sites.
• Sample_type_date_site_season_name.csv - Comma separated file containing Sample, type, date, site and season.

For ease of use, we have also included the original visualization files generated by QIIME2 (using the code in 'combined_scripts.rmd'). These are viewable using the QIIME2 viewer or manually by decompressing them.

• Combined_Scripts.rmd - Rmarkdown containing code for scripts used for data processing and presentation
• demux.qzv
• denoising_stats.qzv
• rep-seqs.qzv
• table-dada2.qzv
• taxa-bar-plots.qzv