Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
  • Loading branch information
AnneliektH authored Dec 31, 2024
1 parent ac03f2a commit be5ecdd
Showing 1 changed file with 4 additions and 0 deletions.
4 changes: 4 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,10 @@ Changing the k-mer size and scaling also have an impact upon sensitivity, specif
#### Parameter tuning for `sourmash taxonomy`
We have set a classification threshold of 75% estimated log containment ("containment ANI" [Rahman Hera, Pierce-Ward, and Koslicki](https://pubmed.ncbi.nlm.nih.gov/37344105/)) to accept classification at a given rank. If this threshold is not met, we move use an LCA approach on the gather results until we have sufficient % match. *This parameter can be modified in the `Snakefile` provided here (TAX_THRESHOLD).*

## Authors
- Anneliek M. ter Horst
- N. Tessa Pierce-Ward

## References

[1] [sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets](https://joss.theoj.org/papers/10.21105/joss.06830)
Expand Down

0 comments on commit be5ecdd

Please sign in to comment.