TRTools: a toolkit for genome-wide analysis of tandem repeats

Nima Mousavi; Jonathan Margoliash; Neha Pusarla; Shubham Saini; Richard Yanicky; Melissa Gymrek

doi:10.1093/bioinformatics/btaa736

TRTools: a toolkit for genome-wide analysis of tandem repeats

Bioinformatics. 2021 May 5;37(5):731-733. doi: 10.1093/bioinformatics/btaa736.

Authors

Nima Mousavi¹, Jonathan Margoliash², Neha Pusarla³, Shubham Saini⁴, Richard Yanicky², Melissa Gymrek^{2

4}

Affiliations

¹ Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, 92093, USA.
² Department of Medicine, University of California San Diego, La Jolla, 92093, USA.
³ Department of Bioengineering, University of California San Diego, La Jolla, 92093, USA.
⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, 92093, USA.

Abstract

Summary: A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.

Availability and implementation: TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Documentation
Gene Library
Genotype
Software*
Tandem Repeat Sequences*

Abstract

Publication types

MeSH terms

Grants and funding