VirusDetect v2

Python rewrite of the VirusDetect plant virus discovery pipeline.

Current package version: 2.0.0a0

Legacy Perl releases remain on the v1 branch and historical v1.2 to v1.8.1 tags. The main branch is the Python v2 line.

Install

Recommended: pixi

pixi install
pixi run virusdetect -- --version
pixi run virusdetect -- tools check

The locked pixi environment currently installs:

• bwa
• samtools
• blast
• hisat2
• spades
• velvet

Alternative: editable Python install

python -m pip install -e .
virusdetect --version

Bioconda status

A Bioconda recipe scaffold is kept in recipes/virusdetect/meta.yaml. It is not published yet. Submission notes are in BIOCONDA.md.

Database

VirusDetect v2 uses a separately distributed database bundle instead of storing the reference database in this repository.

Check the default install target:

virusdetect db path --target

Download the current packaged database:

virusdetect db download
virusdetect db verify

The default download source is the matching GitHub release asset for the current package version:

• release tag: v2.0.0a0
• database bundle: virusdetect-db-2026.04.tar.gz

Database lookup order at runtime:

1. VIRUSDETECT_DB_DIR
2. ./database
3. $CONDA_PREFIX/share/virusdetect/database
4. ~/.local/share/virusdetect/database

Maintainers can build a release bundle from an existing database directory with:

virusdetect db bundle --path <db_dir> --db-version 2026.04

Quick Start

Minimal end-to-end example with the repository test dataset:

pixi run virusdetect -- db download --path ./database
pixi run virusdetect -- run test_data --db-path ./database --stop-after identify_virus -o vd_identify_release

The default v2 assembler is spades. For v1-style comparison work, use:

virusdetect run <reads.fa> --assembler velvet --rm-dup --stop-after identify_virus

Result Files

Stopping after identify_virus produces a Perl-style release directory:

result_<sample>/
  contig_sequences.fa
  contig_sequences.blastn.fa
  contig_sequences.blastx.fa
  contig_sequences.undetermined.fa
  blastn.references.fa
  blastx.references.fa
  blastn.html
  blastx.html
  undetermined_blast.html
  undetermined.html
  blastn.sam
  blastx.sam
  blastn.xls
  blastx.xls

After a successful identify step, the matching <sample>_temp/ directory is removed unless --keep-temp is used.

Current Scope

Implemented on main:

• Python CLI with run, db, and tools
• sample preparation and validation
• virus-reference alignment
• host subtraction
• de novo assembly with spades or velvet
• aligned-contig generation
• combined-contig redundancy reduction
• Python-native blastn and blastx virus identification
• Perl-style release output set for the identify stage

Still not ported from the legacy Perl workflow:

• Bio::Graphics report parity
• full historical siRNA table and layout parity
• exact parity for every legacy HTML formatting detail

Repository Layout

src/virusdetect/   Python package
tests/             Unit tests
tools/             Restored standalone legacy utilities
recipes/           Bioconda recipe scaffold

See CHANGELOG.md for release notes and RELEASE.md for the release checklist.