Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detecti...

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Autores principales: Chiu, Readman, Rajan-Babu, Indhu-Shree, Friedman, Jan M., Birol, Inanc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8361843/
https://www.ncbi.nlm.nih.gov/pubmed/34389037
http://dx.doi.org/10.1186/s13059-021-02447-3
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author Chiu, Readman
Rajan-Babu, Indhu-Shree
Friedman, Jan M.
Birol, Inanc
author_facet Chiu, Readman
Rajan-Babu, Indhu-Shree
Friedman, Jan M.
Birol, Inanc
author_sort Chiu, Readman
collection PubMed
description Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02447-3.
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spelling pubmed-83618432021-08-17 Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences Chiu, Readman Rajan-Babu, Indhu-Shree Friedman, Jan M. Birol, Inanc Genome Biol Software Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02447-3. BioMed Central 2021-08-13 /pmc/articles/PMC8361843/ /pubmed/34389037 http://dx.doi.org/10.1186/s13059-021-02447-3 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Chiu, Readman
Rajan-Babu, Indhu-Shree
Friedman, Jan M.
Birol, Inanc
Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
title Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
title_full Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
title_fullStr Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
title_full_unstemmed Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
title_short Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
title_sort straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8361843/
https://www.ncbi.nlm.nih.gov/pubmed/34389037
http://dx.doi.org/10.1186/s13059-021-02447-3
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