viralunity 1.5.0

A pipeline for viral metagenomics analysis.

ViralUnity

ViralUnity is a tool for analysing viral high-throughput sequencing data. It is a Python package that orchestrates Snakemake workflows for data quality control, taxonomic assignment, and reference genome assembly. ViralUnity runs on *nix systems and can process entire sequencing runs in minimal time on a regular computer.

Full documentation: https://viralunity.readthedocs.io/en/latest/

Installation

Install the ViralUnity CLI from PyPI:

pip install viralunity

conda/mamba is still required at runtime. ViralUnity orchestrates Snakemake, which builds the per-rule tool environments (aligners, classifiers, assemblers) via --use-conda on first run. Make sure conda or mamba is installed and on your PATH; you can pre-build those environments up front with viralunity setup --pipelines all.

To install from source for development instead:

git clone https://github.com/InstitutoTodosPelaSaude/ViralUnity.git
cd ViralUnity
conda env create -n viralunity -f environment.yml
conda activate viralunity
pip install -e .

Per-rule conda environments under viralunity/scripts/envs/ are managed automatically by Snakemake; the top-level environment.yml only installs ViralUnity itself and its core runtime dependencies.

Quick start

Six top-level subcommands are exposed via the viralunity CLI:

viralunity create-samplesheet --input <runs-dir> --output samples.csv
viralunity get-databases all --path databases/
viralunity setup --pipelines all                # pre-build per-rule conda envs
viralunity consensus illumina --sample-sheet samples.csv --reference ref.fasta --output run/
viralunity meta      illumina --sample-sheet samples.csv --kraken2-database <db> --output run/
viralunity build-deacon-index --input host.fasta --output host.dcn

get-databases all grabs the four common databases; the others are separate subcommands (virus-genome, deacon-index, host-genome, nr for meta --run-nr-validation, and the clean-protein-fasta utility) — run viralunity get-databases --help for the full list.

Global options: --log-level {DEBUG,INFO,WARNING,ERROR} and --json-logs (e.g. viralunity --log-level DEBUG meta ...).

Each subcommand has its own --help; the same information is exhaustively documented in the docs/ Sphinx site (rendered on ReadTheDocs at the link above).

Tests

make test

This installs the package in editable mode (if not already installed) and runs the unittest suite under test/. Snakemake dry-run tests live in test/viralunity_dryrun_test.py and use pytest.

Citation

A scientific publication describing this pipeline is being prepared. Meanwhile, please cite this repository. Primary references for upstream tools (fastp, MultiQC, Minimap2, Samtools, BCFtools, BEDtools, gofasta, MEGAHIT, Racon, BLAST, Kraken2, Krona, DIAMOND, Clair3, Medaka, Deacon) are listed in the ReadTheDocs site.

License

MIT — see LICENSE.