ViroSync

ViroSync finds candidate endogenous viral elements (EVEs) in assembled eukaryotic genomes. It detects viral markers, refines boundaries, and provides accepted regions with their evidence.

Workflow

ViroSync runs on CPUs by default. A GPU is not required for the core workflow.

Install ViroSync

ViroSync supports Linux x86-64 and uses Pixi.

git clone https://github.com/NeLLi-team/virosync.git
cd virosync
pixi install --locked
pixi run setup-prodigal-gv
pixi run setup-virosync-resources

Resources download about 6 GB, use about 13 GB when installed, and need about 19 GB during setup. Allow more space for the Pixi environment and results. Native setup builds the pinned Prodigal-GV capacity correction. The installation guide covers its runtime directory and direct Python or console use.

Quick start

pixi run example
cat results/example/batch_summary.tsv

The test-1 row must report status=success, predictions=6, and accepted=1 with resource bundle v1.0.7.

Run your own genomes

pixi run virosync \
  -i genomes/ \
  -o results/my_run \
  --config config/orchestration.yaml \
  -w 4 \
  --threads-per-worker 16

-i accepts one uncompressed .fna, .fasta, or .fa file, a directory of these files, or a text file with one FASTA path per line.

The output root contains batch_summary.tsv with status and counts for each genome. Each genome directory contains:

• phase3_synthesis/virosync_predictions.tsv: accepted EVE calls.
• phase3_synthesis/virosync_predictions.gff3: accepted EVE coordinates and annotations.
• virosync_predictions_detailed.tsv: all candidates and their evidence.
• virosync_repeat_candidates.tsv: same-orientation repeat pairs linked to the detailed candidates, including rejected candidates.

Direct-repeat assessment runs by default and annotates evidence without changing accepted boundaries or confidence tiers. See Outputs for the repeat fields and the root-level output layout of runs that end before Phase 3.

Frameshift-sensitive marker detection is off by default. Add --frameshift-screening to enable it. See the frameshift screening guide for usage and limits.

See the documentation for output details, command options, and optional analyses.

ViroSync 1.0.2 uses resource bundle v1.0.7.

ViroSync is available for non-commercial use under LICENSE.