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*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments

BACKGROUND: Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. FINDINGS: We fi...

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Autores principales: Hörtenhuber, Matthias, Mukarram, Abdul K, Stoiber, Marcus H, Brown, James B, Daub, Carsten O
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069921/
https://www.ncbi.nlm.nih.gov/pubmed/32170312
http://dx.doi.org/10.1093/gigascience/giaa024
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author Hörtenhuber, Matthias
Mukarram, Abdul K
Stoiber, Marcus H
Brown, James B
Daub, Carsten O
author_facet Hörtenhuber, Matthias
Mukarram, Abdul K
Stoiber, Marcus H
Brown, James B
Daub, Carsten O
author_sort Hörtenhuber, Matthias
collection PubMed
description BACKGROUND: Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. FINDINGS: We first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality. CONCLUSIONS: We present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts.
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spelling pubmed-70699212020-03-18 *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments Hörtenhuber, Matthias Mukarram, Abdul K Stoiber, Marcus H Brown, James B Daub, Carsten O Gigascience Research BACKGROUND: Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial. FINDINGS: We first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality. CONCLUSIONS: We present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts. Oxford University Press 2020-03-14 /pmc/articles/PMC7069921/ /pubmed/32170312 http://dx.doi.org/10.1093/gigascience/giaa024 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Hörtenhuber, Matthias
Mukarram, Abdul K
Stoiber, Marcus H
Brown, James B
Daub, Carsten O
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
title *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
title_full *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
title_fullStr *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
title_full_unstemmed *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
title_short *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
title_sort *-dcc: a platform to collect, annotate, and explore a large variety of sequencing experiments
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069921/
https://www.ncbi.nlm.nih.gov/pubmed/32170312
http://dx.doi.org/10.1093/gigascience/giaa024
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