TRACS provides robust estimates of pairwise transmission distances from single isolate, multi-strain and metagenomic samples. It uses an empirical Bayes approach to account for variable sequence coverage and aligns to multiple reference genomes to estimate a lower bound for both the SNP distance and the number of intermediate hosts seperating two samples.
Note: TRACS is not intended to estimate very large SNP distances
TRACS is currently under development and frequent backwards incompatable changes may be made.
Documentation for TRACS can be found here
TRACS can be installed using conda by running
conda install bioconda::tracs
TRACS is a python package and can be installed easily using pip.
pip3 install git+https://github.com/gtonkinhill/tracs
This is all that is needed for the pairwise distance and clustering commands. To generate alignments you will also need to install samtools, minimap2 and htsbox.