Example input and output files for the virus variant caller pipeline

For a description of the pipeline, see the corresponding article in F1000Research (F1000Research 2025, 14:794).

example_config_files.zip: reference annotations for HSV-1 strain 17 and config files describing the input files.

example_bam_files.zip: alignment files (in BAM format) for two replicates each of the ICP0 and vhs knockout mutants.

example_fastq_files.zip: read sequences (in FASTQ format) for two replicates each of the ICP0 and vhs knockout mutants.

example_output.zip: output files for running the pipeline on this dataset, including used software versions and expected runtimes for each step. All steps of the pipeline can be run on a laptop with 16 GB RAM, except for the assembly of inserted sequences with rnaSPAdes, which can be omitted. rnaSPAdes can be run with 32 GB RAM.

files_for_docker_image.zip: files for creating a Docker image pre-configured to run the example. The Docker image is also availabe at the docker hub as carolinefriedel/virus-variant-caller (https://hub.docker.com/r/carolinefriedel/virus-variant-caller)

After downloading and unpacking the zip-archives, adjust the constants in the Watchdog workflow as follows:

<const name="REFERENCE">/path/to/chrHsv1_s17.fa</const><const name="REFERENCE_SNPS">/path/to/reference_snps.txt</const><const name="CONFIG">/path/to/config_strains_HSV1.txt</const><const name="GTF">/path/to/HSV1_Annotation_chrHsv1_s17.gtf</const><const name="samples">/path/to/example_samples.txt</const><const name="replicates">/path/to/example_replicates.txt</const>

where /path/to/ is the directory the content of the archive zip-archives is located in.

Furthermore, change /path/to/ in the example_replicates.txt  and example_samples.txt files to the directory the content of the archive zip-archives is located in.

To run the example with Docker, pull the Docker image from Docker hub with docker pull carolinefriedel/virus-variant-caller:latest (or create a (modified) Docker image using the files in files_for_docker_image.zip) and then run as described at https://hub.docker.com/r/carolinefriedel/virus-variant-caller.

The docker image already contains the files example_config_files.zip, but you need to download the large files in example_bam_files.zip and example_fastq_files.zip. The workflow included in the Docker image already has the constants preconfigured.