diff --git a/README.md b/README.md
index aaa008c0ca9f4e36e378dc82e1db371f91f1e9ff..de8e48f705a6a099d92c99c732e6e83e587f9963 100644
--- a/README.md
+++ b/README.md
@@ -122,7 +122,7 @@ done
 **names in the parameters.yaml file.**  
 These scripts assume that:  
 1. Your data files are stored in `data/raw/`  
-2. Your data files have names like {sample}-trimmed_R1.fastq.gz
+2. Your data files have names like `{sample}.fasta`
 
 If those are both true for your data, use:
 
diff --git a/bin/generate_sample_yaml.sh b/bin/generate_sample_yaml.sh
index a86097b5ee7fd96cbab646393bb579a9c95b9ebd..003aa0e17ee4bdca9b3ad3f58f6e75b07c4cfa72 100644
--- a/bin/generate_sample_yaml.sh
+++ b/bin/generate_sample_yaml.sh
@@ -3,8 +3,8 @@
 # Generate a yaml file for the samples in data/raw
 echo "samples:" > config/samples.yaml
 
-for sample in data/raw/*_R1.fastq.gz
+for sample in data/raw/*.fasta
 do
-    name="$(basename -s "-trimmed_R1.fastq.gz" $sample)"
+    name="$(basename -s ".fasta" $sample)"
     printf "  - ${name}\n"
 done >> config/samples.yaml