PathoPhylo

PathoPhylo is a work-in-progress module to take .tsv files generated by Pathoscope and generate taxonomy and abundance files across all samples

Setting Up PathoPhylo

To set up PathoPhylo do the following:

1. Clone this git repository ie git clone https://github.com/tyden46/PathoPhylo.git

2. Navigate to the getPhylo folder by running cd PathoPhylo/getPhylo

3. Generate libraries by executing bash MakeLibraries.sh

Running PathoPhylo

Requirements:

PathoPhylo requires at least 1 .tsv file from a pathoscope output. These files should be located in the same directory as the run.sh script. Example files are in the getPhylo/input

Command Line Arguments

PathoPhylo is run using the command bash run.sh {MINIMUM_SUM_ABUNDANCE_VALUE} where MINIMUM_SUM_ABUNDANCE_VALUE is a value greater than 0 that represents the minimum summed relative abundance for a genome that you want to consider. This is implemented because Pathoscope will often detect tens of thousands of genomes across samples. Establishing a minimum value of, say, 0.01, will reduce the total number of genomes and significantly improve runtime. If you do not want to set a minimum filter, simply supply a MINIMUM_SUM_ABUNDANCE_VALUE of 0.

Demo

You can run a demo by moving demo input files to the current directory ie mv input/* . and then executing the command bash run.sh 0.01

Output

A file called CombinedTable.txt will be created that contains the relative abundance values across samples for the genomes that passed the MINIMUM_SUM_ABUNDANCE_VALUE threshold.

A file called LineageTable.txt will be created that contains the taxonomic lineage for each the genomes that passed the MINIMUM_SUM_ABUNDANCE_VALUE threshold.