CroCoDeEL is a tool that detects cross-sample contamination (aka well-to-well leakage) in shotgun metagenomic data.
It accurately identifies contaminated samples but also pinpoints contamination sources and estimates contamination rates.
CroCoDeEL relies only on species abundance tables and does not need negative controls nor sample position during processing (i.e. plate maps).
CroCoDeEL is available on bioconda:
conda create --name crocodeel_env -c conda-forge -c bioconda crocodeel
conda activate crocodeel_env
Alternatively, you can use pip:
pip install crocodeel
Finally, you can test that CroCoDeEL is correctly installed with the following command:
crocodeel test_install
CroCoDeEL takes as input a species abundance table in TSV format.
The first column should correspond to species names. The other columns correspond to the abundance of species in each sample.
| species_name | sample1 | sample2 | sample3 | ... |
|---|---|---|---|---|
| species 1 | 0 | 0.05 | 0.07 | ... |
| species 2 | 0.1 | 0.01 | 0 | ... |
| ... | ... | ... | ... | ... |
CroCoDeEL works with relative abundances. The table will automatically be normalized so the abundance of each column equals 1.
Important: CroCoDeEL requires the abundance of subdominant species to be accurately estimated.
We strongly recommend using the Meteor software suite to generate the species abundance table.
Alternatively, you can use sylph although low-level contaminations may go unnoticed.
We advise against the use of other taxonomic profilers (e.g. MetaPhlan4 or mOTUs) that do not meet this requirement according to our benchmarks.
Run the following command to search for cross-sample contamination:
crocodeel search_conta -s species_abundance.tsv -c contamination_events.tsv
CroCoDeEL will report all detected contamination events in the contamination_events.tsv output file.
This TSV file reports for each event the contamination source, the contaminated sample (target) and the estimated contamination rate.
The score (probability) computed by the Random Forest model as well as species specifically introduced by contamination in the target are also given.
Contaminations events can be visually inspected by generating a PDF file consisting in scatterplots.
crocodeel plot_conta -s species_abundance.tsv -c contamination_events.tsv -r contamination_events.pdf
Each scatterplot compares in a log-scale the species abundance profiles of a contaminated sample (x-axis) and its contamination source (y-axis).
The contamination line (in red) highlights species specifically introduced by contamination.
Alternatively, you can search for cross-sample contamination and create the PDF report in one command.
crocodeel easy_wf -s species_abundance.tsv -c contamination_events.tsv -r contamination_events.pdf
CroCoDeEL will probably report false contamination events for samples with similar species abundances profiles (e.g. longitudinal data, animals raised together).
For non-related samples, CroCoDeEL may occasionally generate false positives that can be filtered out by a human-expert.
Thus, we strongly recommend inspecting scatterplots of each contamination event to discard potential false positives.
We will explain how to do it soon.