APDtools is a stand-alone, optional component of the GeneMates package. It offers helper scripts for the measurement and analysis of allelic physical distances (APDs). APDtools implements the following functionality:

• Measurement of APDs in genome assemblies; (measurement)
  • Measurement of APDs from complete genome assemblies; (measurement/ref)
• Accuracy analysis of shortest-path distances (SPDs) by comparing SPDs to true APDs obtained from complete genome assemblies; (accuracy)
• Establishment of relationships between APDs and other biological data for interpretation. (biology)

Please see README.md of each subdirectory for details. Since this toolkit is not an essential part of GeneMates, users may want to develop their own methods to produce the GeneMates-compatible distance table for their specific questions or data.

Dependencies

• R
• Linux bash
• Python (version 3 is recommended)

Terminology

• APD: The physical distance (in bp) between two alleles of one or two genes in a genome assembly.
• SPD: A particular kind of APDs. An SPD equals the number of base pairs between two target alleles following the shortest path in an assembly graph.
  • SPD = 0 when two alleles overlap.
  • The SPD is the true APD in complete (finished-grade) genome assemblies.
  • In draft assembly graphs, we consider SPDs as approximations of true APDs.

Citation

Wan, Y., Wick, R. R., Zobel, J., Ingle, D. J., Inouye, M., & Holt, K. E. (2020). GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. BioRxiv, 2020.02.29.970970. https://doi.org/10.1101/2020.02.29.970970.