Strainify_paper

Simulated datasets

ART Illumina is required to create the simulated datasets Create simulated datasets using the simulate_reads.sh script in each subfolder of the /simulated_exp folder. Please set the art_bin configuration in each script to the path of your ART Illumina binary.

Note: the simulated datasets used in the manuscript will be available on Zenodo soon.

Running Strainify on simulated and mock datasets

Make sure the /Strainify_paper directory and the /Strainify directory are located in the same parent directory. Run Strainify from the /Strainify directory using the following command:

../Strainify_paper/simulated_exp/strainify/run_strainify.sh
../Strainify_paper/4_strain_mock_community/strainify/run_strainify.sh

Note: these scripts assume that you installed Strainify via git. For runtime and memory benchmarking, please uncomment the lines related to the benchmark feature in the Snakefile (lines 47, 78, 88, 104, 117, 133, 143, 154, 166, 176, 190, 209, 224, 243, 262, 283). The runtime and memory benchmarking results analysis scripts are in the strainify_timings directory.

Running StrainScan, StrainR2 and PHLAME on benchmarking datasets

Please find each tool's own folder in this repository and run the scripts inside. Please change the paths in all scripts to match your local setup.

Running Strainify on B. ovatus dataset

All scripts required for this dataset are in the B_ovatus directory.

1. Download the fastq files by running the retrieve_srr.sh script
2. The reference genomes for this dataset are in the all_fastas folder (the script to download the reference genomes is retrieve_fastas.sh and it will download the assemblies in PRJNA544527_AssemblyDetails.txt)
3. Run Strainify via run_strainify.sh. Make sure to run it from the Strainify directory. Please modify the paths in the config.yaml file to match your local setup.
4. To analyze the data, run the following scripts: reorder_srr.py, extract_genome_names.py and stack_plot.py. Please change the paths in these scripts to match your local setup. You will need the srr_list.txt file for the reorder_srr.py script and the assembly_names.tree files for the extract_genome_names.py script.