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AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals
The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI–a...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621952/ https://www.ncbi.nlm.nih.gov/pubmed/37851672 http://dx.doi.org/10.1371/journal.pcbi.1011527 |
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author | Kosiński, Jan G. Żywicki, Marek |
author_facet | Kosiński, Jan G. Żywicki, Marek |
author_sort | Kosiński, Jan G. |
collection | PubMed |
description | The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI–a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals and can be used on custom column-based text files obtained from different data analysis pipelines. Although providing many unique options, AGouTI is straightforward in installation and usage, enabling effortless integration into existing data analysis workflows. |
format | Online Article Text |
id | pubmed-10621952 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-106219522023-11-03 AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals Kosiński, Jan G. Żywicki, Marek PLoS Comput Biol Software The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI–a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals and can be used on custom column-based text files obtained from different data analysis pipelines. Although providing many unique options, AGouTI is straightforward in installation and usage, enabling effortless integration into existing data analysis workflows. Public Library of Science 2023-10-18 /pmc/articles/PMC10621952/ /pubmed/37851672 http://dx.doi.org/10.1371/journal.pcbi.1011527 Text en © 2023 Kosiński, Żywicki https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Software Kosiński, Jan G. Żywicki, Marek AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals |
title | AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals |
title_full | AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals |
title_fullStr | AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals |
title_full_unstemmed | AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals |
title_short | AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals |
title_sort | agouti–flexible annotation of genomic and transcriptomic intervals |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621952/ https://www.ncbi.nlm.nih.gov/pubmed/37851672 http://dx.doi.org/10.1371/journal.pcbi.1011527 |
work_keys_str_mv | AT kosinskijang agoutiflexibleannotationofgenomicandtranscriptomicintervals AT zywickimarek agoutiflexibleannotationofgenomicandtranscriptomicintervals |