From 017301936ee12969e153789c5683b5b767d9f407 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Armin=20To=CC=88pfer?= <atoepfer@pacificbiosciences.com>
Date: Fri, 4 Jun 2021 13:48:06 +0200
Subject: [PATCH] Improve v2.2.0 docs

---
 docs/changelog.md     |  5 +++--
 docs/faq/biosample.md | 24 ++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 2 deletions(-)
 create mode 100644 docs/faq/biosample.md

diff --git a/docs/changelog.md b/docs/changelog.md
index 10a1576..509a6b0 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -7,10 +7,11 @@ nav_order: 99
 # Version changelog
 
  * **2.2.0**:
-   * Add --no-clip to assign a barcode pair, but not clip barcode sequences from reads
+   * Add `--no-clip` to assign a barcode pair, but not clip barcode sequences from reads
    * Output `.consensusreadset.xml` for CCS/HiFi input
-   * Add `--biosample-csv` to assign sample names to barcode pairs
+   * Add `--biosample-csv` to assign [bio sample names](/faq/biosample) to barcode pairs
    * Better help description for `--peek-guess` in combination with `--ccs` and `--isoseq`
+   * Optional [performance improvements](/faq/Speed)
 
  * 2.1.0:
    * SMRT Link v10.1 release
diff --git a/docs/faq/biosample.md b/docs/faq/biosample.md
new file mode 100644
index 0000000..297cec5
--- /dev/null
+++ b/docs/faq/biosample.md
@@ -0,0 +1,24 @@
+---
+layout: default
+parent: FAQ
+title: Bio Sample names
+---
+
+## Associate bio sample names with barcode pairs
+If you want to assign a bio sample name with a barcode pair, you can use the SMRT
+Link feature or directly use it in *lima* version 2.2.0 or later.
+
+For this, please create a CSV file with two columns `Barcodes,Bio Sample`. The
+first column contains the barcode names of the pair; if asymmetric is used,
+only give the pair a single name as the order of the barcodes in a pair is not
+relevant. Example:
+
+    Barcodes,Bio Sample
+    bc1001--bc1001,Alfred
+    bc1002--bc1002,Berthold
+    bc1003--bc1003,Constantin
+    bc1008--bc1008,Holger
+
+Provide this CSV to lima via `--biosample-csv input.csv`.
+
+This will associate the bio sample name to the read group using the `SM` tag.