MOMs-PI_microdiversity_2023

Code used to replicate data analyses in the manuscruipt Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth.

Code

MOMS-PI_analysis.ipynb: code used to analyze CTF, ALTAS, InStrain, gRodon, and PathoFact outputs and metadata and generate plots in Fig. 1-4 and Supplementary Fig. 1-9.

• Fig. 1a: use ALTAS outputs
• Fig. 1b-e: use CTF outputs
• Fig. 2a-f and Fig. 2j: use InStrain outputs based on data from the MOMs-PI study
• Fig. 2h-i: use InStrain outputs based on data from the Relman study (Gotsman et al.)
• Fig. 3a: use ALTAS outputs and InStrain outputs based on data from the MOMs-PI study
• Fig. 3b: use gRoden outputs
• Fig. 3d-f: use InStrain outputs based on data from the MOMs-PI study
• `Fig. 4: use PathoFact outputs
• Supplementary Fig. 2: use ALTAS outputs
• Supplementary Fig. 3 and 4: use InStrain outputs based on data from the MOMs-PI study
• Supplementary Fig. 5a-d: use ALTAS outputs
• Supplementary Fig. 5e: use ALTAS outputs and InStrain outputs based on data from the MOMs-PI study
• Supplementary Fig. 6f-i: use InStrain outputs based on subsampled data (10^5 reads) from the MOMs-PI study
• Supplementary Fig. 6j: use InStrain outputs based on subsampled data (5,000 Gardnerella reads) from the MOMs-PI study
• Supplementary Fig. 6: use ALTAS outputs and InStrain outputs based on data from the MOMs-PI study
• Supplementary Fig. 7: use InStrain outputs based on data from the MOMs-PI study
• Supplementary Fig. 8: use PathoFact outputs
• Supplementary Fig. 9: use metadata

Input data

Input data used for the analyses is published as: Jingqiu Liao, Liat Shenhav, & Tal Korem. (2023). Processed data for Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8150902