A read visualizer to validate structural variants

Quick Start

  1. From the terminal, install the latest version of svviz from pypi: sudo pip install -U svviz
  2. Run the following command: svviz demo

See the documentation for more detailed installation instructions.



svviz visualizes high-throughput sequencing data supporting a structural variant

  • Reconstructs alternate allele sequence

    Reads are aligned against the reconstructed alternate allele sequence – no more awkward visual contortions of the standard reference genome.

  • Supports any read data in BAM format

    Supports short reads, for example from Illumina short-fragment and mate-pair libraries

    Also supports long read data, such as Moleculo (assembled), MinIon or PacBio.

  • Realignment around breakpoints

    Performs a full Smith-Waterman alignment so that reads are aligned across structural variant breakpoints.

  • Interactive browser view

    Supports zooming in and out and shows detailed information about each read upon request.

  • Export to PNG, PDF or SVG

    Export to vector or raster image formats from the browser view or directly from the command-line.

  • Batch mode

    Analyze many putative structural variants simultaneously from an input VCF file.

Long reads

Example heterozygous insertion fully spanned by multiple PacBio reads.

The insertion is shown in blue, replacing a short deleted segment colored orange.

Multiple samples

Example deletion in a trio; based on svviz's output, mother and son appear to be heterozygous for the deletion, while the father is homozygous (only a single read supports the reference, with minimal overlap with the deletion).

Interactive browser interface

Get detailed information about individual reads, SNP positions and more in the browser interface.

More information

svviz was developed by Noah Spies with support from the National Institute of Standards and Technology and the Sidow lab at Stanford University.