GermGenie was specifically designed to analyse 16S data from clinical FFPE specimens, however it can be used to analyse any bacterial sample. GermGenie outputs stacked barplot showing the abundance of every species/genus in your sample. By setting an abundance threshold, any species/genus below the threshold will be added to an 'other' category.
This tool was designed with Oxford Nanopore sequencing reads (ONT), and was not tested with any other sequencing data. The input should be a folder containing one or more samples in a fastq.gz format.
The pipeline is based on EMU. Data is visualized using the Plotly library.
Follow EMU's installation instructions from the repo.
After installing EMU, install GermGenie in the same conda environment.
python -m pip install GermGenieusage: GermGenie [-h] [--threads THREADS] [--threshold THRESHOLD] [--tsv]
fastq output db
EMU wrapper for analyzing and plotting relative abundance from 16S data
positional arguments:
fastq Path to folder containing gzipped fastq files
output Path to directory to place results (created if not
exists.)
db Path to EMU database
optional arguments:
-h, --help show this help message and exit
--threads THREADS, -t THREADS
Number of threads to use for EMU classification
(defaults to 2)
--threshold THRESHOLD, -T THRESHOLD
Percent abundance threshold. Abundances below
threshold will be shown as 'other' (defaults to 1
percent)
--tsv Write abundances to tsv file (abundances.tsv)
Developed by Daan Brackel & Sander Boden @ ATLS-Avans