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Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequenci...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894513/ https://www.ncbi.nlm.nih.gov/pubmed/20562415 http://dx.doi.org/10.1093/bioinformatics/btq269 |
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author | Otto, Thomas D. Sanders, Mandy Berriman, Matthew Newbold, Chris |
author_facet | Otto, Thomas D. Sanders, Mandy Berriman, Matthew Newbold, Chris |
author_sort | Otto, Thomas D. |
collection | PubMed |
description | Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. Availability: The software is available at http://icorn.sourceforge.net Contact: tdo@sanger.ac.uk; cnewbold@hammer.imm.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. |
format | Text |
id | pubmed-2894513 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-28945132010-07-01 Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology Otto, Thomas D. Sanders, Mandy Berriman, Matthew Newbold, Chris Bioinformatics Original Papers Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. Availability: The software is available at http://icorn.sourceforge.net Contact: tdo@sanger.ac.uk; cnewbold@hammer.imm.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2010-07-15 2010-06-18 /pmc/articles/PMC2894513/ /pubmed/20562415 http://dx.doi.org/10.1093/bioinformatics/btq269 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Papers Otto, Thomas D. Sanders, Mandy Berriman, Matthew Newbold, Chris Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology |
title | Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology |
title_full | Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology |
title_fullStr | Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology |
title_full_unstemmed | Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology |
title_short | Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology |
title_sort | iterative correction of reference nucleotides (icorn) using second generation sequencing technology |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894513/ https://www.ncbi.nlm.nih.gov/pubmed/20562415 http://dx.doi.org/10.1093/bioinformatics/btq269 |
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