SynTracker Version 1.2.0

This is an updated version of the SynTracker pipeline, containing all parts of the pipeline in one package (python + R).
The pipeline can be run by one command, using the script syntracker.py.
It contains two modes of execution:

• 'New' mode: for a new run.
• 'Continue' mode: to continue a previous run from the point it has been terminated.

SynTracker Version 1.0.1

This is an updated version of the syntracker pipeline, with updated scripts to allow consistent performance when run on different operating systems.

Version 1.1.0

Changes to simplify and solve file naming procedure, and solve BLAST error resulting from too long fasta headers.

Specific changes:
a. Added script "old_to_new_names.py": changes the file names in the target folder to "Sample.xxx", fasta headers to "contig.yyy", writes the changes to a table, and assigns all sequences to a single file. It is called from find_overlapping_regions.sh.
b. Modified "find_overlapping_regions.sh", to use "old_to_new_names.py" instead of sed command in step 1.
c. Modified "SynTracker.R" to read the table generated by "old_to_new_names.py" and change temporarily assigned sample names back to the original sample names (i.e., file names).
d. Changed "SynTracker_functions.R" to handle the new naming format.