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