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WGLab · Aug 18, 2023 · 966ea0f · 966ea0f
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diff --git a/README.md b/README.md
@@ -28,7 +28,7 @@ NanoCaller can be installed using Docker or Conda. The easiest way to install is
 or using Docker:
 
 ```
-VERSION="3.3.0"
+VERSION="3.4.1"
 docker pull genomicslab/nanocaller:${VERSION}
 ```
 Please refer to [Installation](docs/Install.md) for instructions regarding installing NanoCaller through other methods.

diff --git a/docs/Install.md b/docs/Install.md
@@ -46,7 +46,7 @@ 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="3.0.0"
+VERSION="3.4.1"
 docker run genomicslab/nanocaller:${VERSION} NanoCaller --help
 ```
 
@@ -62,7 +62,7 @@ docker run nanocaller NanoCaller --help
 ## Singularity
 For instructions regarding Singularity installation, please visit [Singularity website] (https://sylabs.io/guides/3.7/user-guide/quick_start.html).
 ```
-VERSION="3.0.0"
+VERSION="3.4.1"
 singularity pull docker://genomicslab/nanocaller:${VERSION}
 singularity exec -e --pwd /app nanocaller_${VERSION}.sif NanoCaller --help
-```
+```
diff --git 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=3.0.0
+VERSION=3.4.1
 docker run -it -v ${PWD}:'/mnt/'  genomicslab/nanocaller:${VERSION} NanoCaller \
 --bam /mnt/HG002.Guppy_4.2.2_prom.bam --ref /mnt/GRCh38.fa --prefix HG002 --preset ont \
 --output /mnt/calls --cpu $CPU --exclude_bed hg38 --wgs_contigs chr1-22XY

diff --git a/docs/Usage.md b/docs/Usage.md
@@ -13,7 +13,7 @@ Please check the [NanoCaller Docker Hub repository](https://hub.docker.com/repos
 
 NanoCaller can call variants from whole genome or several chromosomes using a single command `NanoCaller`. Assuming all your input files are in a folder `YOUR_INPUT_DIR`, and you want to use `YOUR_OUTPUT_DIR` to store the results. You can use `--regions` or `--bed` to specify regions for variant calling, otherwise all contigs in the input BAM file will be used. 
 ```
-VERSION=3.0.0
+VERSION=3.4.1
 docker run \
 -v 'YOUR_INPUT_DIR':'/input/' \
 -v 'YOUR_WORKING_DIR':'/output/' \
@@ -216,4 +216,4 @@ Some important options to keep in mind when using NanoCaller:
 - `-nbr_t` option is sensitive to sequencing type so choose this accordingly.
 - `-ins_t` and `del_t` are insertion and deletion frequency thresholds are per haplotype. Default values are slightly higher due to high error in ONT reads, but these thresholds can be lowered for CCS reads.
 - CLR reads have incredibly low insertion and deletion freqencies in a pileup due highly variable placement of indels by aligners. To detect indels on CLR reads, you would need to set low frequency threhsolds, which leads to a huge increase in runtime.
-- `--enable_whatshap` flag can improve SNP calling performance for PacBio reads.
+- `--enable_whatshap` flag can improve SNP calling performance for PacBio reads.