The Genome Resolved Open Watersheds database (GROWdb): A functional microbiome catalog crowdsourced from North American rivers

This repository contains data for version 1 of the Genome Resolved Open Watersheds database (GROWdb), along with data for the manuscript describing GROWdb: 

"A functional microbiome catalog crowdsourced from North American rivers"

Mikayla A. Borton, Bridget B. McGivern, Kathryn R. Willi, Ben J. Woodcroft, Annika C. Mosier, Ted Bambakidis, Derick M. Singleton, Filipe Liu, Janaka N. Edirisinghe, José P. Faria, Rebecca A. Daly, Amy E. Goldman, Michael J. Wilkins, Ed K. Hall, Christa Pennacchio, Simon Roux, Emiley A. Eloe-Fadrosh, Matthew B. Sullivan, Christopher S. Henry, Elisha M. Wood-Charlson, Matthew R.V. Ross, Christopher S. Miller, Byron C. Crump, James C. Stegen, Kelly C. Wrighton

Annotation datasets

• annotations.tsv.zip: raw DRAM annotations of 2,093 unique MAGs in GROWdb
• metabolism_summary.xlsx: DRAM distillate summary of genome annotations 
• genes.fna.zip: nucleotide sequences of genes in 2,093 unique MAGs in GROWdb, with gene identifiers corresponding to those in annotations.tsv.zip

Antibiotic resistance genes (ARGs) dataset

• ARGS_genes_rgi.txt: Output of Resistance Gene Identifier containing list of predicted ARGs
• AMR_expression_by_sample.csv: metatranscriptomic expression of identified ARGs by category

Expression (Metatranscriptome) Data Tables

• GENES_geTMM_norm.counts.rpk_edger_zenodo.csv: geTMM values per gene filtered to genes in at least 10% of samples
• BINS_norm.counts.rpk_edger.mean_atLeast20_zenodo.csv: mean geTMM values per genome filtered to genes in at least 10% of samples and to bins with at least 20 genes expressed

Phylogenetic Tree Files

• GROW_nxr/nar_tree.pdf: pdf format of phylogenetic tree of nxr and nar
• GROW_pmoA_amoA_tree.pdf: pdf format of phylogenetic tree of pmoA and amoA
• bipartitionsBranchLabels.nxr-nar_seqs_for_tree_aligned.faa_mode_low.renamed: newick format of phylogenetic tree of nxr and nar
• bipartitionsBranchLabels.amoA_pmoA_seqs_for_tree_aligned.faa_mode_low.renamed: newick format of phylogenetic tree of pmoA and amoA