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SIQ: easy quantitative measurement of mutation profiles in sequencing data
With the emergence of CRISPR-mediated genome editing, there is an increasing desire for easy-to-use tools that can process and overview the spectra of outcomes. Here, we present Sequence Interrogation and Quantification (SIQ), a simple-to-use software tool that enables researchers to retrieve, data-...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9442499/ https://www.ncbi.nlm.nih.gov/pubmed/36071722 http://dx.doi.org/10.1093/nargab/lqac063 |
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author | van Schendel, Robin Schimmel, Joost Tijsterman, Marcel |
author_facet | van Schendel, Robin Schimmel, Joost Tijsterman, Marcel |
author_sort | van Schendel, Robin |
collection | PubMed |
description | With the emergence of CRISPR-mediated genome editing, there is an increasing desire for easy-to-use tools that can process and overview the spectra of outcomes. Here, we present Sequence Interrogation and Quantification (SIQ), a simple-to-use software tool that enables researchers to retrieve, data-mine and visualize complex sets of targeted sequencing data. SIQ can analyse Sanger sequences but specifically benefit the processing of short- and long-read next-generation sequencing data (e.g. Illumina and PacBio). SIQ facilitates their interpretation by establishing mutational profiles, with a focus on event classification such as deletions, single-nucleotide variations, (templated) insertions and tandem duplications. SIQ results can be directly analysed and visualized via SIQPlotteR, an interactive web tool that we made freely available. Using insightful tornado plot visualizations as outputs, we illustrate that SIQ readily identifies sequence- and repair pathway-specific mutational signatures in a variety of model systems, such as nematodes, plants and mammalian cell culture. |
format | Online Article Text |
id | pubmed-9442499 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-94424992022-09-06 SIQ: easy quantitative measurement of mutation profiles in sequencing data van Schendel, Robin Schimmel, Joost Tijsterman, Marcel NAR Genom Bioinform High Throughput Sequencing Methods With the emergence of CRISPR-mediated genome editing, there is an increasing desire for easy-to-use tools that can process and overview the spectra of outcomes. Here, we present Sequence Interrogation and Quantification (SIQ), a simple-to-use software tool that enables researchers to retrieve, data-mine and visualize complex sets of targeted sequencing data. SIQ can analyse Sanger sequences but specifically benefit the processing of short- and long-read next-generation sequencing data (e.g. Illumina and PacBio). SIQ facilitates their interpretation by establishing mutational profiles, with a focus on event classification such as deletions, single-nucleotide variations, (templated) insertions and tandem duplications. SIQ results can be directly analysed and visualized via SIQPlotteR, an interactive web tool that we made freely available. Using insightful tornado plot visualizations as outputs, we illustrate that SIQ readily identifies sequence- and repair pathway-specific mutational signatures in a variety of model systems, such as nematodes, plants and mammalian cell culture. Oxford University Press 2022-09-05 /pmc/articles/PMC9442499/ /pubmed/36071722 http://dx.doi.org/10.1093/nargab/lqac063 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | High Throughput Sequencing Methods van Schendel, Robin Schimmel, Joost Tijsterman, Marcel SIQ: easy quantitative measurement of mutation profiles in sequencing data |
title | SIQ: easy quantitative measurement of mutation profiles in sequencing data |
title_full | SIQ: easy quantitative measurement of mutation profiles in sequencing data |
title_fullStr | SIQ: easy quantitative measurement of mutation profiles in sequencing data |
title_full_unstemmed | SIQ: easy quantitative measurement of mutation profiles in sequencing data |
title_short | SIQ: easy quantitative measurement of mutation profiles in sequencing data |
title_sort | siq: easy quantitative measurement of mutation profiles in sequencing data |
topic | High Throughput Sequencing Methods |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9442499/ https://www.ncbi.nlm.nih.gov/pubmed/36071722 http://dx.doi.org/10.1093/nargab/lqac063 |
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