bedapub / HBVouroboros

HBVouroboros automates sequencing-based HBV genotyping and expression profiling

HBVouroboros automates sequencing-based HBV genotyping and expression profiling

HBVouroboros uses RNA-sequencing reads to infer HBV genotype, quantify HBV transcript expression, and perform variant calling of HBV genomes.

HBVouroboros, distributed under the GPL-3 license, is available at https://github.com/bedapub/HBVouroboros.

Installation and usage

Download the source code

git clone https://github.com/bedapub/HBVouroboros.git

Setup conda environment

## setup conda environment
cd envs; conda env create; cd -
## in case it has been installed, use the command below to update
## conda env update
conda activate HBVouroboros

Run an example

An out-of-box example can be run by starting the snakemake pipeline.

snakemake -j 99 --configfile config/config_template.yaml --use-envmodules ## use --use-conda if no R module is present

Run the pipeline with your own data

Create a config file by copying the template.

cp config/config_template.yaml config/config.yaml

Next, modify the config/config.yaml file to specify a sample annotation file, and make other changes if necessary.

Run HBVouroboros using unmapped reads from a Biokit output directory

This feature has been disabled now. It may be activated in the future.

Validating the sensitivity and specificity of HBVouroboros with RNAsim2

We created RNAsim2, a RNA-seq simulator to validate the sensitivity and specificity of HBVouroboros. See RNAsim2/README.md for details.

Known issues and solutions

What to do if conda environment initialization takes too long?

Above we use the default conda solver. If you suffer from slow speed of conda, consider using mamba, which is a drop-in replacement of conda.

If you met more issues, please raise them using the Issues function of GitHub.