– Create histograms of predicted amplicons for primer pairs


Using amplicons files (generated with, this module will generate histogram(s) showing the predicted amplicon sizes. If a taxonomy mapping file is passed, the histograms will be separated according to domain (archaea, bacteria, and eukaryotic).

Usage: [options]

Input Arguments:



-f, --amplicons_filepath
Target amplicons files. Separate multiple files with a colon.


-o, --output_dir
Specify output directory for amplicons and reads. [default: .]
-r, --all_files
Generate histograms for all files ending with _amplicons.fasta in the directory specified with the -f parameter [default: False]
-t, --taxa_map
Filepath to taxonomy mapping file, used to separate graphs according to domain. [default: None]


There will be an output graph in postscript format with the same root name as the input _amplicons.fasta file for each _amplicons.fasta file passed.

Standard Example usage (create a histogram from an amplicon file, output to the current directory): [options] {-f amplicons_filepath }

Test for all _amplicons.fasta files in current directory, pass a taxonomy mapping file so histograms are plotted according to domain, and output to amplicons_graph directory: -f . -r -t taxonomy_mapping.txt -o amplicons_graph

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