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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
river, microbiome, metagenome, metatranscriptome, microbial
river, microbiome, metagenome, metatranscriptome, microbial
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