Explain --single-end

docs/changelog.md

@@ -10,7 +10,11 @@ nav_order: 99
    * SMRT Link v13.0 release
    * Add `--overwrite-biosample-name` option for double demux
    * Add `sa`, `sm`, and `sx` tags
-   * Fixes for `--single-end` 
+   * Fixes for `--single-end`
+
+ * 2.7.1:
+   * SMRT Link v12.0 release
+   * Allow `--single-end` to only score to score only one flank
 
  * 2.6.0:
    * Support SEGMENT read type

docs/faq/adapter-types.md

@@ -59,5 +59,5 @@ A lower than ~40% percentage indicates decreased local accuracy during
 sequencing leading to adapter sequences not being found. If a high percentage
 of ZMWs is molecularly missing adapters, you should improve library prep.
 
-## How can I demultiplex data with one adapter only being barcoded?
+## How can I demultiplex data with one adapter only being barcoded in CLR data?
 Use `--single-side`.

docs/faq/barcoded-adapter.md

@@ -10,11 +10,24 @@ depicted in the [barcode design overview](barcode-design). One minor
 disadvantage is that the ligation might not be as efficient as with standard
 SMRTbell adapters, leaving some molecules only with one adapter. As barcoded
 adapter designs are inherently symmetric, we implemented ways to recover the
-demultiplexed yield from one-sided barcoded molecules with ease.
+demultiplexed yield from one-sided barcoded molecules with ease, using
+`--single-end`.
 
 As the first step, generate HiFi data with *ccs* v6.3.0 or later. This version
 will store [additional tags per
 records](https://ccs.how/faq/missing-adapters.html), indicating if the molecule
 has missing adapters on either side. The second step is to use the new
 `--hifi-preset SYMMETRIC-ADAPTERS` introduced with *lima* v2.5.0, [described
-here](/faq/hifi-presets). That's it.
+here](/faq/hifi-presets). That's it. All of this done automatically starting
+with Revio.
+
+## What is `--single-end`?
+The option `--single-end` was introduced with Revio in SMRT Link v12.0 and
+*lima* v2.7.1. It allows to only score one side of a HiFi read, if the other
+flank is molecularly missing a barcoded adapter. It is controlled by
+`--min-end-score` and is set by default for both SYMMETRIC HiFi presets. If you
+see a barcode not matching one side of the HiFi read at all, check the [`ma` and
+`ac` tags](https://ccs.how/faq/missing-adapters.html) to see if the read is
+missing the read is missing the barcoded adapter on one side and the
+`--single-end` heuristic got activated. In *lima* v2.9.0 we improved this option
+to further reduce barcode miscalls.

docs/index.md

@@ -26,7 +26,7 @@ for information on Installation, Support, License, Copyright, and Disclaimer.
 Version **2.9.0**: [Full changelog here](/changelog)
 
 ## What's new
- * Improved precision using [`--hifi-preset SYMMETRIC-ADAPTERS`](/faq/hifi-presets) or `SYMMETRIC`
+ * Increased HiFi preset precision by improving [`--single-end`](https://lima.how/faq/barcoded-adapter.html#what-is---single-end)
  * Undo demultiplexing via [`lima-undo`](/faq/undo)
 
 ## Get started