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All Your Base: a fast and accurate probabilistic approach to base calling
The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms t...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053729/ https://www.ncbi.nlm.nih.gov/pubmed/22377270 http://dx.doi.org/10.1186/gb-2012-13-2-r13 |
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author | Massingham, Tim Goldman, Nick |
author_facet | Massingham, Tim Goldman, Nick |
author_sort | Massingham, Tim |
collection | PubMed |
description | The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms the basis of a base calling method which improves on the best existing base callers, especially when comparing the number of error-free reads. The novel algorithms implemented in All Your Base (AYB) are comparable in speed to other competitive base-calling methods, do not require training data and are designed to be robust to gross errors, producing sensible results where other techniques struggle. AYB is available at http://www.ebi.ac.uk/goldman-srv/AYB/. |
format | Online Article Text |
id | pubmed-4053729 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40537292014-06-13 All Your Base: a fast and accurate probabilistic approach to base calling Massingham, Tim Goldman, Nick Genome Biol Method The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms the basis of a base calling method which improves on the best existing base callers, especially when comparing the number of error-free reads. The novel algorithms implemented in All Your Base (AYB) are comparable in speed to other competitive base-calling methods, do not require training data and are designed to be robust to gross errors, producing sensible results where other techniques struggle. AYB is available at http://www.ebi.ac.uk/goldman-srv/AYB/. BioMed Central 2012 2012-02-29 /pmc/articles/PMC4053729/ /pubmed/22377270 http://dx.doi.org/10.1186/gb-2012-13-2-r13 Text en Copyright © 2012 Massingham et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Method Massingham, Tim Goldman, Nick All Your Base: a fast and accurate probabilistic approach to base calling |
title | All Your Base: a fast and accurate probabilistic approach to base calling |
title_full | All Your Base: a fast and accurate probabilistic approach to base calling |
title_fullStr | All Your Base: a fast and accurate probabilistic approach to base calling |
title_full_unstemmed | All Your Base: a fast and accurate probabilistic approach to base calling |
title_short | All Your Base: a fast and accurate probabilistic approach to base calling |
title_sort | all your base: a fast and accurate probabilistic approach to base calling |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053729/ https://www.ncbi.nlm.nih.gov/pubmed/22377270 http://dx.doi.org/10.1186/gb-2012-13-2-r13 |
work_keys_str_mv | AT massinghamtim allyourbaseafastandaccurateprobabilisticapproachtobasecalling AT goldmannick allyourbaseafastandaccurateprobabilisticapproachtobasecalling |