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Performance evaluation of six popular short-read simulators
High-throughput sequencing data enables the comprehensive study of genomes and the variation therein. Essential for the interpretation of this genomic data is a thorough understanding of the computational methods used for processing and analysis. Whereas “gold-standard” empirical datasets exist for...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9905089/ https://www.ncbi.nlm.nih.gov/pubmed/36496447 http://dx.doi.org/10.1038/s41437-022-00577-3 |
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author | Milhaven, Mark Pfeifer, Susanne P. |
author_facet | Milhaven, Mark Pfeifer, Susanne P. |
author_sort | Milhaven, Mark |
collection | PubMed |
description | High-throughput sequencing data enables the comprehensive study of genomes and the variation therein. Essential for the interpretation of this genomic data is a thorough understanding of the computational methods used for processing and analysis. Whereas “gold-standard” empirical datasets exist for this purpose in humans, synthetic (i.e., simulated) sequencing data can offer important insights into the capabilities and limitations of computational pipelines for any arbitrary species and/or study design—yet, the ability of read simulator software to emulate genomic characteristics of empirical datasets remains poorly understood. We here compare the performance of six popular short-read simulators—ART, DWGSIM, InSilicoSeq, Mason, NEAT, and wgsim—and discuss important considerations for selecting suitable models for benchmarking. |
format | Online Article Text |
id | pubmed-9905089 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-99050892023-02-08 Performance evaluation of six popular short-read simulators Milhaven, Mark Pfeifer, Susanne P. Heredity (Edinb) Article High-throughput sequencing data enables the comprehensive study of genomes and the variation therein. Essential for the interpretation of this genomic data is a thorough understanding of the computational methods used for processing and analysis. Whereas “gold-standard” empirical datasets exist for this purpose in humans, synthetic (i.e., simulated) sequencing data can offer important insights into the capabilities and limitations of computational pipelines for any arbitrary species and/or study design—yet, the ability of read simulator software to emulate genomic characteristics of empirical datasets remains poorly understood. We here compare the performance of six popular short-read simulators—ART, DWGSIM, InSilicoSeq, Mason, NEAT, and wgsim—and discuss important considerations for selecting suitable models for benchmarking. Springer International Publishing 2022-12-10 2023-02 /pmc/articles/PMC9905089/ /pubmed/36496447 http://dx.doi.org/10.1038/s41437-022-00577-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Milhaven, Mark Pfeifer, Susanne P. Performance evaluation of six popular short-read simulators |
title | Performance evaluation of six popular short-read simulators |
title_full | Performance evaluation of six popular short-read simulators |
title_fullStr | Performance evaluation of six popular short-read simulators |
title_full_unstemmed | Performance evaluation of six popular short-read simulators |
title_short | Performance evaluation of six popular short-read simulators |
title_sort | performance evaluation of six popular short-read simulators |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9905089/ https://www.ncbi.nlm.nih.gov/pubmed/36496447 http://dx.doi.org/10.1038/s41437-022-00577-3 |
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