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Significantly improving the quality of genome assemblies through curation
Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a multitude of research projects. Despite the ever-advancing improvements in data generation, assembly algorithms and pipeline...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794651/ https://www.ncbi.nlm.nih.gov/pubmed/33420778 http://dx.doi.org/10.1093/gigascience/giaa153 |
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author | Howe, Kerstin Chow, William Collins, Joanna Pelan, Sarah Pointon, Damon-Lee Sims, Ying Torrance, James Tracey, Alan Wood, Jonathan |
author_facet | Howe, Kerstin Chow, William Collins, Joanna Pelan, Sarah Pointon, Damon-Lee Sims, Ying Torrance, James Tracey, Alan Wood, Jonathan |
author_sort | Howe, Kerstin |
collection | PubMed |
description | Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a multitude of research projects. Despite the ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near error-free genome assemblies for eukaryotes. Whilst working towards improved datasets and fully automated pipelines, assembly evaluation and curation is actively used to bridge this shortcoming and significantly reduce the number of assembly errors. In addition to this increase in product value, the insights gained from assembly curation are fed back into the automated assembly strategy and contribute to notable improvements in genome assembly quality. We describe our tried and tested approach for assembly curation using gEVAL, the genome evaluation browser. We outline the procedures applied to genome curation using gEVAL and also our recommendations for assembly curation in a gEVAL-independent context to facilitate the uptake of genome curation in the wider community. |
format | Online Article Text |
id | pubmed-7794651 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-77946512021-01-13 Significantly improving the quality of genome assemblies through curation Howe, Kerstin Chow, William Collins, Joanna Pelan, Sarah Pointon, Damon-Lee Sims, Ying Torrance, James Tracey, Alan Wood, Jonathan Gigascience Review Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a multitude of research projects. Despite the ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near error-free genome assemblies for eukaryotes. Whilst working towards improved datasets and fully automated pipelines, assembly evaluation and curation is actively used to bridge this shortcoming and significantly reduce the number of assembly errors. In addition to this increase in product value, the insights gained from assembly curation are fed back into the automated assembly strategy and contribute to notable improvements in genome assembly quality. We describe our tried and tested approach for assembly curation using gEVAL, the genome evaluation browser. We outline the procedures applied to genome curation using gEVAL and also our recommendations for assembly curation in a gEVAL-independent context to facilitate the uptake of genome curation in the wider community. Oxford University Press 2021-01-09 /pmc/articles/PMC7794651/ /pubmed/33420778 http://dx.doi.org/10.1093/gigascience/giaa153 Text en © The Author(s) 2021. Published by Oxford University Press GigaScience. 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 | Review Howe, Kerstin Chow, William Collins, Joanna Pelan, Sarah Pointon, Damon-Lee Sims, Ying Torrance, James Tracey, Alan Wood, Jonathan Significantly improving the quality of genome assemblies through curation |
title | Significantly improving the quality of genome assemblies through curation |
title_full | Significantly improving the quality of genome assemblies through curation |
title_fullStr | Significantly improving the quality of genome assemblies through curation |
title_full_unstemmed | Significantly improving the quality of genome assemblies through curation |
title_short | Significantly improving the quality of genome assemblies through curation |
title_sort | significantly improving the quality of genome assemblies through curation |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794651/ https://www.ncbi.nlm.nih.gov/pubmed/33420778 http://dx.doi.org/10.1093/gigascience/giaa153 |
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