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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-...

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Autores principales: van Schendel, Robin, Schimmel, Joost, Tijsterman, Marcel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
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.
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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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