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dib-lab / genome-grist

map Illumina metagenomes to genomes!
https://dib-lab.github.io/genome-grist/
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What should we benchmark? #263

Open ccbaumler opened 1 year ago

ccbaumler commented 1 year ago

Following the same process as sourmash-bio/sourmash#2410, we will benchmark the genome-grist workflow with a combination of the six sequences listed in the sourmash-bio/sourmash#2410. My instinct is to:

  1. Run each sequences alone
  2. Run a variety of sequences from small to large sets
  3. Run the all six together

We could also include benchmarking different databases across the steps above.

ctb commented 1 year ago

I don't think that genome-grist has any individually expensive steps or computationally complex scripts that are part of it; it's just the workflow overall that involves an awful lot of steps, much like charcoal. That may change your benchmarking strategy.