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leeHom: adaptor trimming and merging for Illumina sequencing reads
The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another. Challenges for the processing of such reads are the accurate ident...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191382/ https://www.ncbi.nlm.nih.gov/pubmed/25100869 http://dx.doi.org/10.1093/nar/gku699 |
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author | Renaud, Gabriel Stenzel, Udo Kelso, Janet |
author_facet | Renaud, Gabriel Stenzel, Udo Kelso, Janet |
author_sort | Renaud, Gabriel |
collection | PubMed |
description | The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another. Challenges for the processing of such reads are the accurate identification of the adaptor sequence and accurate reconstruction of the original sequence most likely to have given rise to the observed read(s). We introduce an algorithm that removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. Our algorithm is faster, and provides a more accurate reconstruction of the original sequence for both simulated and ancient DNA data sets, than other approaches. leeHom is released under the GPLv3 and is freely available from: https://bioinf.eva.mpg.de/leehom/ |
format | Online Article Text |
id | pubmed-4191382 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-41913822015-04-02 leeHom: adaptor trimming and merging for Illumina sequencing reads Renaud, Gabriel Stenzel, Udo Kelso, Janet Nucleic Acids Res Methods Online The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another. Challenges for the processing of such reads are the accurate identification of the adaptor sequence and accurate reconstruction of the original sequence most likely to have given rise to the observed read(s). We introduce an algorithm that removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. Our algorithm is faster, and provides a more accurate reconstruction of the original sequence for both simulated and ancient DNA data sets, than other approaches. leeHom is released under the GPLv3 and is freely available from: https://bioinf.eva.mpg.de/leehom/ Oxford University Press 2014-10-13 2014-08-06 /pmc/articles/PMC4191382/ /pubmed/25100869 http://dx.doi.org/10.1093/nar/gku699 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. 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 | Methods Online Renaud, Gabriel Stenzel, Udo Kelso, Janet leeHom: adaptor trimming and merging for Illumina sequencing reads |
title | leeHom: adaptor trimming and merging for Illumina sequencing reads |
title_full | leeHom: adaptor trimming and merging for Illumina sequencing reads |
title_fullStr | leeHom: adaptor trimming and merging for Illumina sequencing reads |
title_full_unstemmed | leeHom: adaptor trimming and merging for Illumina sequencing reads |
title_short | leeHom: adaptor trimming and merging for Illumina sequencing reads |
title_sort | leehom: adaptor trimming and merging for illumina sequencing reads |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191382/ https://www.ncbi.nlm.nih.gov/pubmed/25100869 http://dx.doi.org/10.1093/nar/gku699 |
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