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Dependencies

Step 20-wp requires the PCLA_proteins.txt.gz file, which contains the protein clusters. The pipeline will download this file automatically as follows:

wget --no-check-certificate http://www.ic.unicamp.br/~meidanis/PUB/Mestrado/2020-Oliveira/PCLA_proteins.txt.gz && mv PCLA_proteins.txt.gz 20-wp

We provide a specification file spec-file-linux-64 to replicate our environment. Nevertheless, these are the required packages to run the pipeline:

conda install -c conda-forge r-base
conda install -c conda-forge r-ape
conda install -c conda-forge r-codetools
conda install -c conda-forge jupyterlab
conda install -c bioconda r-phangorn
conda install -c bioconda ncbi-genome-download
conda install -c bioconda bioconductor-ggtree
conda install -c r r-irkernel

In addition, install the Quartet package by typing install.packages('Quartet') from within R. (Note that the quartet package available in Conda is not the same.)

Generating the results for Shigella and E. coli genomes

To generate the results for a rearrangement distance, run the following:

conda create --name my_env --file spec-file-linux-64      # create conda env from spec file
conda activate my_env                                     # activate env
make esche_shige DIST=${DIST} OUTGRP=EF_ATCC35            # run pipeline for rank distances

Here, ${DIST} is either rank, rankindl, rankc, or dcj. For the rank distance, we recommend using rankc, which is more efficient than the other two. The outputs are the Newick files containing the phylogenetic trees in 70-tree. The code to generate the figures and comparison metrics is available in the jupyter notebook 70-tree/analysis.ipynb.

Running just make will display a helper message on options for the parameters. A required dependency for the proper execution of the pipeline is the content in the config folder:

  • test.csv: metadata of 4 Vibrio strains used for testing purposes;
    • OUTGRP=AS_VS224
  • esche_shige.csv: metadata of Shigela and E. coli genomes, e.g. accession number, annotation, etc;
    • OUTGRP=EF_ATCC35
  • esche_shige_short.tree: reference phylogenetic tree.

Generating the results for simulated data

See the folder simulation.