Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
With sourmash-bio/sourmash_plugin_branchwater#430, we can now use lists of .sig.zip files and/or standalone manifest CSVs.
So, I ran the benchmarks with sourmash-bio/sourmash_plugin_branchwater#471, which includes both sourmash-bio/sourmash_plugin_branchwater#430 and some other speedups, and got a really nice outcome - it's faster than ever, although it also uses more memory because (presumably) it's keeping many more metagenomes in memory simultaneously, due to the speed.
* this run used sig.zip files and manifest CSVs in the benchmarking