Merge pull request #17 from PacificBiosciences/update-min-score-docs

Update min-score and hifi presets docs

docs/faq/filter-input.md

@@ -14,7 +14,7 @@ step. The default is `0`, meaning deactivated.
 
 ## `--min-score`
 Threshold for the average barcode score of the leading and trailing ends.
-ZMWs with barcode score below `N` are omitted. The default is `0`.
+ZMWs with barcode score below or equal to `N` are omitted. The default is `0`.
 It is advised to set it to `26` for CLR and `80` for HiFi.
 
 ## `--min-passes`

docs/faq/hifi-presets.md

@@ -6,17 +6,13 @@ title: HiFi Presets
 
 ## HiFi presets
 With v2.5.0 we introduced the concept of recommended parameter presets called
-`--hifi-preset`. All preset use
-
-    --ccs --min-score 80 --min-end-score 50 --min-ref-span 0.75
-
-in addition they differ as following
+`--hifi-preset`. 
 
 |        Preset        |              Definition               |
 | -------------------- | ------------------------------------- |
-| `SYMMETRIC`          | `--same`                              |
-| `SYMMETRIC-ADAPTERS` | `--same --ignore-missing-adapters`    |
-| `ASYMMETRIC`         | `--different --min-scoring-regions 2` |
+| `SYMMETRIC`          | `--ccs --min-score 0 --min-end-score 80 --min-ref-span 0.75 --same --single-end` |
+| `SYMMETRIC-ADAPTERS` | `--ccs --min-score 0 --min-end-score 80 --min-ref-span 0.75 --same --ignore-missing-adapters --single-end` |
+| `ASYMMETRIC`         | `--ccs --min-score 80 --min-end-score 50 --min-ref-span 0.75 --different --min-scoring-regions 2` |
 
 For barcoded adapter libraries, `SYMMETRIC-ADAPTERS` will increase demultiplexed
 yield. More info under [barcoded adapter FAQ](/faq/barcoded-adapter)