Scripts in support of the publication "Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries"
Open source pre-print publication is available at bioRxiv
Publication is in press at mSystems
An open-source program enabling marker gene analysis from metagenomic data is available at https://github.com/alexcritschristoph/RPxSuite
Nucleotide sequences of genome sets used in this study are available at https://doi.org/10.6084/m9.figshare.c.4508162.v1
In the JupyterNotebooks folder is a list of Jupiter Notebooks. These can be viewed using Jupiter, and have the details on how much of the analysis was performed.
Notebook 1 documents how to load the results of FastANI in a standardized manner.
Notebook 2 documents how to use the output from Notebook 1 to generate Figure 1
Notebook 3 documents how to load the results of dnds_from_drep.py, which is needed to make Figure 2. dnds_from_drep.py is a python script that is to be run on the output from from dRep when run using the --S_algorithm goANI option.
Notebook 4 documents how to run popCOGent in a hack-y way. Methods are largely copy pasted from the original code here, based on the following publication. This notebook allows you to run only the part of the program that is needed to generate Figure 2
Notebook 5 takes the results of Notebooks 3 and 4 to generate Figure 2.
Notebooks 6 and 7 document how species delineation thresholds and Figure 3 were generated.