Hybracter v0.4.0 Benchmarking Output

This dataset contains: The subsampled FASTQ files used to benchmarking Hybracter (https://github.com/gbouras13/hybracter). Benchmarking Output for Hybracter v0.4.0 vs Unicycler v0.5.0 vs Dragonflye v1.1.2 on these files. The full benchmarking code and explanation is available https://github.com/gbouras13/hybracter_benchmarking. DOI: https://zenodo.org/doi/10.5281/zenodo.10157987. The `hybracter_benchmarking_fastqs.tar.gz` file will contain all FASTQs (gzipped) used to benchmarking `hybracter`. The `hybracter_benchmarking_results_v0.4.0.tar.gz` file will contain: `BENCHMARKS` - contains the time etc benchmarking for each run (sample x tool) `DNADIFF` - contains raw chromosome Dnadiff results for each run (sample x tool) `DNADIFF_PARSED_OUTPUT` - contains parsed chromosome Dnadiff results for each sample `DNADIFF_PLASMIDS` - contains plasmid Dnadiff results for each run (sample x tool) `DNADIFF_PARSED_OUTPUT_PLASMID` - contains parsed plasmid Dnadiff results for each sample `REAL` - this contains all the actual output for each assembler. The following 5 directories will contain the all the raw output with subdirectories for each sample: `HYBRACTER_HYBRID_OUTPUT` `HYBRACTER_LONG_OUTPUT` Note there will also be a `LAST` subdirectory in the `HYBRACTER_HYBRID_OUTPUT` and `HYBRACTER_LONG_OUTPUT`. The output contained in it are the sample, but where hybracter is run with `--logic last`. These were mostly done to test the functionality, not so much from a benchmarking perspective. Additionally, it should have `HYBRACTER_HYBRID_OUTPUT_REAL_BULK` - this contains the output for the 12 Lerminiaux et al isolates assembled using `hybracter hybrid` with modified config file `bulk_assemble_lerminiaux_config.yaml`. `DRAGONFLYE_HYBRID_OUTPUT` `DRAGONFLYE_LONG_OUTPUT` `UNICYCLER_OUTPUT` It will also contain a number of other subdirectories `_SUMMARIES`, `_PLASMIDS`, `_CHROMOSOMES` with parsed summary outputs and parsed specific plasmids and chromosome assemblies for Unicycler and Dragonflye (this made the assessment a lot easier and automated).