TRGT

Tandem repeat genotyping tool for HiFi sequencing data

TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat and visualization of reads overlapping the repeats.

Version information

Current version: 5.0.0.

For a complete changelog, see the changelog or the git history.

Active development warning

Please note that TRGT is still under active development. We anticipate some changes to the input and output file formats of TRGT.

Availability

• TRGT Linux binary is available here

Repeat catalogs

In order to use TRGT, you need to specify which repeats you want it to analyze. Here are some repeat catalogs that you can use.

• STRchive is a high-quality catalog containing definitions of known pathogenic repeats. It is described here.
• “Adotto” genome-wide repeat catalog described in the original TRGT paper and here.
• Genome-wide repeat catalog containing isolated tandem repeats and variation clusters described here.
• Catalog of pathogenic repeats originally distributed with TRGT has been deprecated; please use STRchive.

Joint analysis of multiple samples

TRGT outputs VCFs containing repeat alleles from each region in the repeat catalog. To facilitate analysis of repeats across multiple samples, VCFs can be either merged into a multi-sample VCF using the merge sub-command or converted into a database using the TDB tool (formerly called TRGTdb). TDB offers many advantages over multi-sample VCFs, including simpler data extraction, support for queries, and reduced file sizes.

Documentation

• Tutorials
  • Introductory tutorial: non-interactive and interactive versions
  • Interpreting TRGT plots
  • Analyzing PureTarget data
• Reference
  • Command-line interface
  • Repeat definition file
  • Spanning BAM generated by TRGT
  • VCF files generated by TRGT
  • Remote file support
  • Merging TRGT VCFs
  • Deepdive subcommand
  • Validating repeat catalogs

Need help?

If you notice any missing features, bugs, or need assistance with analyzing the output of TRGT, please don’t hesitate to reach out by email or open a GitHub issue.

Support information

TRGT is currently in active development and is intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that TRGT lives up to the quality that PacBio strives for, we make no warranty regarding this software.

As TRGT is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any TRGT release. Please report all issues through GitHub instead. We make no warranty that any such issue will be addressed, to any extent or within any time frame.

Citation

If you use TRGT, please consider citing the paper:

Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung W, Bi C, Farrow E, Wenger A, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson D, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. 2024

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