Prediction/classification of the origin of a metagenomics sample.

Installation

$ conda install -c etetoolkit -c bioconda -c maxibor sourcepredict

Example

$ wget wget https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/test/dog_test_sample.csv -O dog_test_sample.csv
$ sourcepredict -t 6 dog_test_sample.csv
Step 1: Checking for unknown proportion
  == Sample: ERR1915662 ==
	Adding unknown
	Normalizing (GMPR)
	Computing Bray-Curtis distance
	Performing MDS embedding in 2 dimensions
	KNN machine learning
	Training KNN classifier on 6 cores...
	-> Testing Accuracy: 1.0
	----------------------
	- Sample: ERR1915662
		 known:98.61%
		 unknown:1.39%
  == Sample: ERR1915662_copy ==
	Adding unknown
	Normalizing (GMPR)
	Computing Bray-Curtis distance
	Performing MDS embedding in 2 dimensions
	KNN machine learning
	Training KNN classifier on 6 cores...
	-> Testing Accuracy: 1.0
	----------------------
	- Sample: ERR1915662_copy
		 known:98.61%
		 unknown:1.39%
Step 2: Checking for source proportion
	Computing weighted_unifrac distance on species rank
	TSNE embedding in 2 dimensions
	KNN machine learning
	Performing 5 fold cross validation on 6 cores...
	Trained KNN classifier with 10 neighbors
	-> Testing Accuracy: 0.99
	----------------------
	- Sample: ERR1915662
		 Canis_familiaris:96.14%
		 Homo_sapiens:2.44%
		 Soil:1.42%
	- Sample: ERR1915662_copy
		 Canis_familiaris:96.14%
		 Homo_sapiens:2.44%
		 Soil:1.42%
Sourcepredict result written to dog_test_sample.sourcepredict.csv

Documentation

The documentation of SourcePredict is available here: sourcepredict.readthedocs.io

Sourcepredict source file

• The sources were obtained with the Kraken based pipeline included in this repository, using the MiniKraken2_v2_8GB.
• The default source file is here data/modern_gut_microbiomes_sources.csv
• The label file for this source file is here data/modern_gut_microbiomes_sources.csv

Environments included in the default source file

• Homo sapiens gut microbiome
• Canis familiaris gut microbiome
• Soil microbiome

Updating the source file

To update the sourcefile with new kraken results, see the instruction in the dedicated Jupyter notebook