VAMPIRE - VAriation and Motif Patterns In tandem REpeats

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VAMPIRE - VAriation and Motif Patterns In tandem REpeats#

VAMPIRE is a unified framework for de novo tandem repeat (TR) annotation and analysis. It systematically characterizes copy number variation, motif variation and structural variation within TR arrays.

By representing TR arrays as hierarchical motif compositions and quantifying copy-number changes, motif substitutions, and array restructuring across samples, VAMPIRE transforms raw sequence data into standardized, interpretable, and queryable repeat-variation matrices. Through its AnnData-based data model, VAMPIRE enables seamless integration with downstream analysis workflows.

Read the documentation. Open an issue or create a pull request if you would like to contribute.

Version: v0.4.2

Quick Start#

Not sure where to begin? Select the workflow that matches your data:

Annotate multiple TRs on genome

De novo TR discovery from genome assembly.

scan
Annotate single TR locus across population

TR variation profiling across samples at target loci.

anno

Walkthrough Analysis#

Ready to dive deeper? Follow these step-by-step examples:

Single locus#

STR/VNTR analysis across populations

Example analysis of 69 bp VNTR in the intron of the gene WDR7 across human population.

STR/VNTR across populations
Centromere and satellites analysis and visualization

Example analysis and visualization of the centromere region of T2T-CHM13v2.0 chromosome 1.

Centromere and Satellites

News#

2026-06-22 - VAMPIRE v0.4.2 Release#

  • Fixed a bug in src/vampire/_anno.py.

  • Added GitHub Actions workflow to build and push Docker images to zikunyang/vampire-tr automatically on version tags.

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