Commit fd0c3da3 authored by Aaron Petkau's avatar Aaron Petkau

Added basic benchmarking info

parent 1bb82b98
# Benchmarking
A number of datasets have been used to benchmark the runtime of SNVPhyl across a range of scenarios. These are as follows.
## Manuscript datasets
The datasets from the [SNVPhyl manuscript][] were run on a single machine using the Docker version. The following table presents the run times (to go from sequence reads to a phylogeny) and data sizes of each case.
| Case | Number of genomes | Total size of reads (GB) | Runtime (min) |
|:---------------------:|:-----------------:|:------------------------:|:-------------:|
| Simulated data | 4 | 1.4 | 16 |
| SNV density filtering | 11 | 13 | 21 |
| Salmonella Heidleberg | 59 | 40 | 192 |
The **Simulated data** case was run using a set of simulated reads through SNVPhyl, based off of *E. coli* str. Sakai (NC_002695) and two plasmids (NC_002128 and NC_002127). The other two cases were run with real-world data. The **SNV density filtering** case was run using a set of 11 *Streptococcus pneumoniae* genomes through SNVPhyl, in particular the runtime presented was recorded when no SNV density filtering was applied. The **Salmonella Heidleberg** case was run using a set of 59 *Salmonella* Heidleberg genomes, and in particular the runtime presented corresponds to the case of using a minimum coverage threshold of 10X while keeping all other parameters at default values.
The machine used to run each of these cases was an Intel Xeon CPU @ 3.33 GHz, 16 cores, and 24 GB of memory. More details on the methods can be found in the [SNVPhyl manuscript][], or in [snvphyl-validations][] github project.
[docker version of SNVPhyl]: ../install/docker
[SNVPhyl manuscript]: http://biorxiv.org/content/early/2016/12/10/092940
[snvphyl-validations]: https://github.com/apetkau/snvphyl-validations
......@@ -21,6 +21,7 @@ pages:
- 'Escherichia coli': 'examples/escherichia-coli.md'
- Comparison:
- 'ASM NGS Challenge 2015': 'comparison/asm-ngs-2015.md'
- 'Benchmarking': 'comparison/benchmarking.md'
- Developer:
- 'Upgrading SNVPhyl Toolshed' : 'developer/upgrading.md'
- Citation/Contact: 'citation.md'
......
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