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Table 2 Results files generated by WATERS for further analyses.

From: Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

Results file Contents Purpose
aligned_sequences.fas All seqs pre-OTUHunter QC; Alignment
bad_infernal_sequences.fas Seqs un-alignable by Infernal QC
chimeras.fas Seqs removed by Mallard QC
coordinates_Rank_abundance.csv x,y coordinates for rank-abundance Create graphs
coordinates_Rarefaction.csv x,y coordinated for rarefaction Create graphs
graph_*_variable.xgmml Similarities between libraries based on shared OTUs Cytoscape
graph-Rank_Abundance.bip/.ps Printed graph of rank-abundance curves View graphs
graph-Rarefaction.bip/.ps Printed graph of rarefaction curves View graphs
otu-table.txt Counts of OTUs and diversity indices at each cutoff and metadata variable Graph OTUs; diversity metrics
sequences-*.fas One representative seq for each OTU found Alignment
short_sequences.fas Short seqs that did not pass cut off QC
tree_*.txt Phylogenetic tree of representatives with taxonomy information Unifrac
Dendroscope
unifrac_*_variable.txt "Environment file" for Unifrac; OTU abundance and library info Unifrac
workflow.trace Provenance file written by Kepler describing the worklow run QC
  1. Fourteen different types of results files can be generated from one run of WATERS in its complete configuration. * represents the cutoffs used in OTUHunter, by default 97 and 99 percent similarity, which will generate two different files at each cutoff used. Abbreviations: Seq(s), sequence(s); QC, Quality Control; OTU, Operational Taxonomic Unit.