Corbata: CORe microBiome Analysis Tools

Input File

Summary Table Files

The input you will need for these analyses is essentially an NxM table, where N is the number of samples, and M are each of the taxonomic classifications, or categories.  Our input file format, the "summary table", also contains an extra column for the total.  This extra column helps us confirm, as a checksum, that all the columns are consistent if any transformations have been made, as well as helping to determine if the file has been normalized.   

The summary table is a tab delimited text file which may be opened in Microsoft Excel or OpenOffice Calc.  The first row contains the header information which includes the fields named: "sample id", "total", and an entry for each taxon.  Thus, there will be M+2 columns in the summary file table.  The first column contains the sample ids for each sample in the cohort.  The second column contains a sum of all the counts across the row for that sample.  There will be N+1 rows in the summary table file, because the first row is the header information.

Output Files

PDF files

The output files are generally Adobe PDF files.

Supplemental Tables

Sometimes tables, in the form of text files that may underlie the plots, may be generated.  These are provided to help you get the exact values for the positions of the various elements in the plots.  Additional descriptions for these will be provided in the examples for each analysis.  The text tables were laid out to be read into MS Excel or OO Calc, so header names are usually provided in the text files. Please check the documentation embedded in the source code, that is displayed when the script is invoked without any arguments.