Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils.

This repository holds the final data products from metagenomics processing of bacteria and viruses from the article : "Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils"

Contents: 

• LU_metadata.csv: information on the samples
• soil_chemistry.txt: physicochemical information on samples
• *_len.csv: tables containing the length information for annotated genes, divided by database. These are used to calculate RPKM abundances from count tables. 
• BACTERIA
• ko_table, ko_unknown, ko2level, ko_description: count table of KEGG annotations, total counts for unnanotated genes, match of ko number to level and description
• all_bracken.csv: count table of taxonomic bacterial annotations using kraken2 and bracken
• mags_tax.csv: taxonomy assignments to MAGs (metagenome assembled genomes)
• mags_count_table.csv: abundante table of MAGs in counts
• ags_result, gc_mean, gc_variance: functional traits results, average genome size, and gc content
• lu_c_count, lu_n_count, card_d0, metals_count_table: abundance tables of genes annotated with Cazy (carbon), Ncydb (nitrogen), CARD (antibiotic resistance genes), and Bacmet (heavy metal resistance genes)
• VIRUS
• amg_summary.csv: results from AMG annotation with DRAM-V, filtered to keep genes of interest
• genomad_virus_summary.tsv: viral taxonomy annotations with geNomad
• virus_len.txt: length of inferred viruses (used for calculation of RPKM from count tables)
• all_host_prediction_to_genus.csv: virus host annotation with IPhop
• final_checkv.tsv: table of final viral inferences with quality estimates
• viral_species_count_table.txt: abundance table of infered viral contigs in counts