Table 2

Results files generated by WATERS for further analyses.

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


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.

Hartman et al. BMC Bioinformatics 2010 11:317   doi:10.1186/1471-2105-11-317

Open Data