This repo is a collection of four example datasets for the "personal comparison" version of the ConSpeciFix pipeline. The input files are located in the folder #_name_pre and the resulting file structure can be found and downloaded from #_name_post.zip.
To run the ConSpeciFix pipeline for a folder of input genomes, follow the instructions in the ConSpeciFix readme for "Personal Comparison". The command to launch the process is:
python runner_personal.py /absolute/path/to/1_example_pre/
All examples of output are available here:
- 1_dengue_post.zip (17M)
- 2_enterovirusMix_post.zip (7.5M)
- 3_bacteria_post.zip (502M)
- 4_zika_post.zip (148M)
A note on time: The ConSpeciFix process does a large number of analyses, not all of which are crucial to the final verdict of deciding which strains are members of the species. The strain maps in particular takes a lot of time and memory (n^2 on size of input), and can be optionally turned off in the config.py file by setting GENERATE_GENE_MAPS = False. With this flag set, examples one and two should complete within 10 minutes on most modern machines.
- Dengue: This first example (located in
1_dengue_preand1_dengue_post) is a collection of samples from the Dengue virus. This example should run quickly and report all strains being members of the species. - Enterovirus: An example of two divergent species in one sample. Only the Enterovirus G are labeled as being members of the species, as well as one strain mislabeled as F.
- Bacteria: An example on a longer genome. Will take proportionally longer to run.
- Zika: An example with more than 100 strains, and demonstrates how extra strains are removed if too many are present.