diff --git a/docs/Install.md b/docs/Install.md
index 90d0e4c..c71efe9 100644
--- a/docs/Install.md
+++ b/docs/Install.md
@@ -9,7 +9,7 @@ For instructions regarding Docker installation, please visit [Docker website](ht
 ### 1) via Docker Hub (preferred)
 You can pull NanoCaller docker images from Docker Hub by specifiying a version number.  
 ```
-VERSION="0.3.0"
+VERSION="0.3.1"
 docker run genomicslab/nanocaller:${VERSION} python NanoCaller.py --help
 ```
 
@@ -26,10 +26,10 @@ docker run  nanocaller python NanoCaller.py --help
 If you want to use NanoCaller Docker image saved in a tar file, download the image file by specifying a version number and use `docker load`.
 
 ```
-VERSION="0.3.0"
+VERSION="0.3.1"
 wget https://github.com/WGLab/NanoCaller/releases/download/v${VERSION}/nanocaller_docker.tar.gz
 docker load --input nanocaller_docker.tar.gz
-docker run  nanocaller python NanoCaller.py --help
+docker run genomicslab/nanocaller:${VERSION}  python NanoCaller.py --help
 ```
 
 
diff --git a/docs/ONT Case Study.md b/docs/ONT Case Study.md
index a6c7c05..61795b3 100644
--- a/docs/ONT Case Study.md	
+++ b/docs/ONT Case Study.md	
@@ -39,7 +39,7 @@ GM24385_2_Guppy_4.2.2_prom.fastq.gz  GM24385_3_Guppy_4.2.2_prom.fastq.gz -t $CPU
 samtools index HG002.Guppy_4.2.2_prom.bam -@ $CPU
 
 # run nanocaller
-VERSION=0.3.0
+VERSION=0.3.1
 docker run -it -v ${PWD}:'/mnt/'  genomicslab/nanocaller:${VERSION} python NanoCaller_WGS.py \
 -bam /mnt/HG002.Guppy_4.2.2_prom.bam -ref /mnt/GRCh38.fa -prefix HG002 \
 -o /mnt/calls -cpu $CPU --exclude_bed hg38
diff --git a/docs/Usage.md b/docs/Usage.md
index 74208ad..e349e4d 100644
--- a/docs/Usage.md
+++ b/docs/Usage.md
@@ -5,7 +5,7 @@
 
 For whole genome variant calling, or calling variants on several chromosomes, use `NanoCaller_WGS.py` to call variants. Assuming all your input files are in a folder `YOUR_INPUT_DIR`, and you want to use `YOUR_OUTPUT_DIR` to store the results. 
 ```
-VERSION=0.3.0
+VERSION=0.3.1
 docker run -itd \
 -v 'YOUR_INPUT_DIR':'/input/' \
 -v 'YOUR_WORKING_DIR':'/output/' \
@@ -23,7 +23,7 @@ python NanoCaller_WGS.py \
 
 For calling variants on single chromosomes, use `NanoCaller.py` to call variants. Assuming all your input files are in a folder `YOUR_INPUT_DIR`, and you want to use `YOUR_OUTPUT_DIR` to store the results. 
 ```
-VERSION=0.3.0
+VERSION=0.3.1
 docker run -itd \
 -v 'YOUR_INPUT_DIR':'/input/' \
 -v 'YOUR_WORKING_DIR':'/output/' \