ExId16S validation

Script to validate the python package ExId16S

General information

• Author: Kaitlin Weber
• Commissioned by: Rijksinstituut voor Volksgezondheid en Milieu (RIVM)

About this script

This python script validates the results of ExId16S, by comparing the summary file kreport with the results of the gold standards 16S rDNA sequencing and WGS sequencing. The script creates bar plots, for comparison with the gold standards. In addition, the script also has the option to compare the results of the custom made database with a standard SILVA database.

Installation

1. Clone the repository:

git clone https://github.com/Kaitlinweber/exid16s_validation

2. Enter the directory with the pipeline and install the conda environment:

cd exid16s_validation
conda env install -f envs/vaidation_env.yaml

Required parameters

• -i, --input Kraken summary kreport from ExId16S results, based on the custom made database.
• -w, --wgs Kraken summary kreport obtained from Kraken2 and Bracken with Whole Genome Sequencing data.
• -s, --sample_list Excel sheet with 16S rDNA Sanger sequencing results, with the sample number, genus name and species name in a seperate column.
• -o, --output Pathway to output directory, if directory does not exists, directory will be created

Optional parameters

• -si, --silva For the comparison of the created database with the SILVA database, the pathway to the SILVA database Kraken kreports can be given here

The base command to run this script

python validation.py -i [path/to/input/dir/ExId16S] -w [path/to/input/dir/WGS] -s [path/to/input/dir/16S_sequencing] -o [path/to/output/dir]