## Examples of benchmarking from lab [An example of using snakemake for benchmarking](https://github.com/dib-lab/2022-branchwater-benchmarking/issues/3) [The benchmark output files from the above repo](https://github.com/dib-lab/2022-branchwater-benchmarking/tree/main/benchmarks) [The use of `mprof` which profile memory usage on `sourmash gather`](https://github.com/sourmash-bio/sourmash/issues/2340) [Jessica's benchmarking process](https://github.com/jessicalumian/ep-streaming) [`sourmash compare` memory needs profiling!!](https://github.com/sourmash-bio/sourmash/issues/2299) ## Tools for benchmarking software Flamegraph - [Repo](https://github.com/brendangregg/FlameGraph) - [Flamegraph](https://www.brendangregg.com/flamegraphs.html) - [Memory profile flamegraph](https://www.brendangregg.com/FlameGraphs/memoryflamegraphs.html) - [differential flamegraph](https://www.brendangregg.com/blog/2014-11-09/differential-flame-graphs.html) - [Rust edition (Read the bottom)](https://github.com/flamegraph-rs/flamegraph) py-spy - [documentation](https://pypi.org/project/py-spy/) - [repo](https://github.com/benfred/py-spy) timeit - [documentation](https://docs.python.org/3/library/timeit.html) snakemake - [Benchmarking a workflow](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#benchmark-rules) - [Explanation of benchmarking variables](https://stackoverflow.com/questions/46813371/meaning-of-the-benchmark-variables-in-snakemake) - [Git repo organization for snakemake workflow](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#distribution-and-reproducibility) - [Catalog of workflow](https://snakemake.github.io/snakemake-workflow-catalog/?rules=true) - [example of properly organized workflow](https://github.com/snakemake-workflows/dna-seq-varlociraptor/)
Examples of benchmarking from lab
An example of using snakemake for benchmarking
The benchmark output files from the above repo
The use of
mprofwhich profile memory usage onsourmash gatherJessica's benchmarking process
sourmash comparememory needs profiling!!Tools for benchmarking software
Flamegraph
py-spy
timeit
snakemake