Dataset_S1.Smutans.tar.gz

31 Streptococcus mutans genomes reconstructed from metagenomic data

Dataset_S2.Ssobrinus.tar.gz

315 Streptococcus sobrinus genomes reconstructed from metagenomic data

Dataset_S3.SPARSE.tar.gz

Python Scripts
1. SPARSE_ml.py	Fit machine learning models on SPARSE results
2. SPARSE_curve.py	Calculate rarefaction curve on SPARSE results
3. SPARSE_dist.py	Calculate Euclidian distances of samples and species
Source Files
1. SPARSE.species.profile	SPARSE results
2. SPARSE.samples	Oral sources of samples
Batch workflow
1. commands.bash	All the commands to generate results
Outputs
1. SPARSE.species.profile.SVM	Support Vector Machine results. Figure 2
2. SPARSE.species.profile.PCA	PCA results. Figure S1
3. SPARSE.species.profile.UMAP	UMAP results. Figures 1A & S1
4. SPARSE.species.profile.curves	Rarefaction curves. Figure 5
5. SPARSE.species.profile.sample.dist	Abundance distances of samples for NJ tree. Figure 1B
6. SPARSE.species.profile.taxon.dist	Abundance distances of species for NJ tree. Figures 4 & S2

Use:

 SPARSE_ml.py --help
 SPARSE_curve.py --help
 SPARSE_dist.py --help

To obtain detailed help on the scripts.