Protist_barcode_MAG_correspondence

Online Supplement to "On the relationship between protist metabarcoding and protist metagenome-assembled genomes"

R_scripts

calculation :

• sim_calc.R - calculate pairwise correspondence between the features in simulated datasets
• sim_data_gen.R - generate simulated datasets that mimic SMAG or V9 data
• taxogroup_distr.R - generate summary statistics on SMAG and V9 taxonomy data
• Evil_Shuffle.R - shuffling of SMAG and V9 datasets with subsequent correspondence calculation
• zero_abundance_SMAGs_list.R , station_intersect_counts.R - minor summary stats on SMAG and V9 abundance datasets
• script_summary_propr_calc.R , script_summary_shuffle_stats.R , script_summary_sim_stats.R - generate summary tables from correspondence estimates of SMAG and V9 data, shuffled SMAG and V9 data and simulated data, correspondingly

downstream :

• breakpoint_detection.Rmd - generate breakpoint_summary_rho_cor.tsv
  • scenario_assignation_for_candidate_pairs.Rmd - assign scenarios to the manually curated list of SMAG-V9 OTU pairs

plots :

• scripts used to produce plots

data

data_inputs :

• taxa_counts.tsv - input file with SMAG and V9 taxonomic subset sizes
• avg_abund_V9.tsv , V9_var_vector.tsv - average abundance counts and variance of abundance counts for V9 data, used by sim_data_gen.R as input parameters for metaSPARSim simulation
• TAGs-18S-V4_NAME-PROJ-MAT-READ-CAB_nico.list - custom list of sample names for SMAG and V9 data, used to match V9 samples with SMAG samples
• Online_data_available_elsewhere - list with download and reference links previously published and used in this study available online
• final_taxa_ext_genus.csv - taxonomy dictionary of SMAGs and V9

calc_outputs :

• all_scores.zip - correspondence for all SMAG - V9 OTU pairs in all taxonomic subset for all metrics
• rand_all_scores_relabund_inv_ext_shuff_scratch.zip , all_scores_relabund_simulation_matr.zip - example outputs produced by Evil_Shuffle.R and sim_calc.R, correspondingly (Note they are not exhaustive, but just an instance of the output produced!)
• to_plot_*_shuffle1.tsv - summary stats used to generate plots

summary_calcs:

• summary_propr_calc_stats*.tsv , summary_shuffle_stats*.tsv , summary_sim_stats_*.tsv - summary of outputs produced by script_summary_propr_calc.R , script_summary_shuffle_stats.R script_summary_sim_stats.R, correspondingly
• se_summary_shuffle_stats*.tsv , se_summary_sim_stats*.tsv - - summary of se of estimates from the multiple replicates of outputs produced by script_summary_shuffle_stats.R script_summary_sim_stats.R, correspondingly

downstream_outputs :

• breakpoint_summary_rho_cor.tsv - results of automatic filtering by criteria applied for breakpoint detection
• Candidate_pairs-for_R_script_scatterplot_corrected_Pairs_automated.csv - manually curated list of SMAG-V9 OTU pairs
• Scenarios_auto_assigned_candidate_pairs.csv - manually curated list of SMAG-V9 OTU pairs with automatically assigned scenarios
• blastSAGs.tsv - blast output for reference genome- SAG control
• plots.zip - various plots, along with miscellaneous data for plot generation.

manuscript_figs_n_code

• svg of main figures
• source LaTeX data for the manuscript pdf