diff --git a/README.md b/README.md
index 372c1a4..1a1b59a 100644
--- a/README.md
+++ b/README.md
@@ -52,8 +52,14 @@ and placed in the given SAM record tag (`RX` by default).  Similarly, the sample
 barcode bases from the given read will be placed in the `BC` tag.
 
 Metadata about the samples should be given as a headered metadata TSV file with
-two columns 1. `sample_id` - the id of the sample or library. 2. `barcode` - the
-expected barcode sequence associated with the `sample_id`.
+at least the following two columns present:
+
+1. `sample_id` - the id of the sample or library. 
+2. `barcode` - the expected barcode sequence associated with the `sample_id`.
+
+For reads containing multiple barcodes (such as dual-indexed reads), all barcodes
+should be concatenated together in the order they are read and stored in the 
+`barcode` field.
 
 The read structures will be used to extract the observed sample barcode, template
 bases, and molecular identifiers from each read.  The observed sample barcode
diff --git a/src/bin/commands/demux.rs b/src/bin/commands/demux.rs
index e2bec29..53842b0 100644
--- a/src/bin/commands/demux.rs
+++ b/src/bin/commands/demux.rs
@@ -518,9 +518,14 @@ impl DemuxMetric {
 /// default).  Similarly, the sample barcode bases from the given read will be placed in the `BC`
 /// tag.
 ///
-/// Metadata about the samples should be given as a headered metadata TSV file with two columns
-/// 1. `sample_id` - the id of the sample or library.
+/// Metadata about the samples should be given as a headered metadata TSV file with at least the 
+/// following two columns present:
+/// 
+/// 1. `sample_id` - the id of the sample or library. 
 /// 2. `barcode` - the expected barcode sequence associated with the `sample_id`.
+/// 
+/// For reads containing multiple barcodes (such as dual-indexed reads), all barcodes should be 
+/// concatenated together in the order they are read and stored in the `barcode` field.
 ///
 /// The read structures will be used to extract the observed sample barcode, template bases, and
 /// molecular identifiers from each read.  The observed sample barcode will be matched to the