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

GROWdb Global MAG files

5986_99ID_drep_global.tar.gz: zipped file of dereplicated MAG files (n=5,986) from global freshwater analysis of 9,798 MAGs

GlobalMAG_Inventory.xlsx: Inventory of 9,798 MAGs used in global analysis