Visualisation and processing of template switch mutations

Twitcher Workbench

Twitcher Workbench is a browser and visualisation app, as well as a post-processing and analysis toolkit for Twitcher CSV output. It provides a browser-based web UI and the command-line interface twb cli.

The Workbench allows annotating the Twitcher output with biological meta-data, including gene and repeat overlap, sequence complexity, and TSM event types; it can deduplicate/group the data, merging (and counting) multi-copy TSM loci from BAM data, or identifying (and genotyping) shared TSM loci within joined family data. The processed data can then be filtered using the rich column information and the presence/absence of sample individuals in grouped events. These processing and filtering functionalities are available both in the web UI and the CLI application. The CSV handling is highly efficient and tested to work with more than 1M rows.

The browser-based web UI lets you analyse and visualise the processed CSV data, and click any row to visualize the event with Twitcher, JBrowse, Vienna DNA fold, or raw BAM slice tools.

Features

Twitcher Workbench web UI provides:

  • Interactive visualization of Twitcher-identified TSM events
  • User-created filter presets
  • Export/import filter presets as JSON for sharing and CLI reuse
  • Support for bundled or uploaded reference genomes, gene annotations, and repeat-masking files

In addition to the shared features, twb cli provides:

  • Filter-only mode for applying exported web presets to already processed CSV files
  • Interactive and non-interactive label assignment, such as ‘HG002’ -> ‘Son’

Documentation