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)
- Measurement of APDs from complete genome assemblies; (
- 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.