Skip to content

Commit

Permalink
fix typo
Browse files Browse the repository at this point in the history
  • Loading branch information
Meena Chakraborty committed Oct 31, 2022
1 parent efa7930 commit 4ad275b
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ This section contains a description of the additional parameters in the config f
* `cov_thresh_viral` (default `0.1`). This parameter can range from 0 to 1 and specifies a genome coverage requirement for a viral species to be considered a "true positive" in a sample. For example, if this parameter is 0.1, that means that for a viral species to be considered a true positive in a sample, at least one genome of the species must be at least 10% covered by sample reads.
* Each genome's coverage is estimated by dividing:
* The number of unique minimizers in the genome that are covered by sample reads, by
* The total number of unique minimizers in the genome.
* The total number of minimizers in the genome.
* *Terminology note* - minimizers are very similar to kmers; for a more detailed description of what they are, please see [the Kraken2 paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1891-0).
* `minimizer_thresh_viral` (default `0`). This parameter can take any value >= 0 and specifies an additional requirement for a viral species to be considered true positive in a sample. E.g., if this parameter is 10, that means at least one genome of the species must have 10+ of its unique minimizers covered by sample reads.
* `cov_thresh_bacterial` and `minimizer_thresh_bacterial` are the analogous parameters for filtering bacterial species.
Expand Down

0 comments on commit 4ad275b

Please sign in to comment.