scholarly journals ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

2019 ◽  
Author(s):  
Egor Dolzhenko ◽  
Viraj Deshpande ◽  
Felix Schlesinger ◽  
Peter Krusche ◽  
Roman Petrovski ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Broad Class ◽  
Source Code ◽  
Computational Method ◽  
Dna Repeats ◽  
Link Type ◽  
Sequence Graph ◽  
Version 2.0 ◽  
Short Tandem

SummaryWe describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci.Availability and implementationExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/[email protected]

scholarly journals ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions

2019 ◽  
Vol 35 (22) ◽  
pp. 4754-4756 ◽  
Author(s):  
Egor Dolzhenko ◽  
Viraj Deshpande ◽  
Felix Schlesinger ◽  
Peter Krusche ◽  
Roman Petrovski ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Broad Class ◽  
Source Code ◽  
Computational Method ◽  
Supplementary Information ◽  
Dna Repeats ◽  
Supplementary Data ◽  
Sequence Graph ◽  
Version 2.0 ◽  
Short Tandem

Abstract Summary We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. Availability and implementation ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. Supplementary information Supplementary data are available at Bioinformatics online.

Analysis of short tandem repeat (STR) HUMVWA in the Spanish population

1994 ◽  
Vol 65 (3) ◽  
pp. 169-175 ◽  
Author(s):  
Jose A. Lorente ◽  
Miguel Lorente ◽  
Bruce Budowle ◽  
Mark R. Wilson ◽  
Enrique Villanueva
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Spanish Population ◽  
Short Tandem

NIST Mixed Stain Study 3:  Signal Intensity Balance in Commercial Short Tandem Repeat Multiplexes

2004 ◽  
Vol 76 (23) ◽  
pp. 6928-6934 ◽  
Author(s):  
David L. Duewer ◽  
Margaret C. Kline ◽  
Janette W. Redman ◽  
John M. Butler
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Signal Intensity ◽  
Short Tandem
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