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OMWare: a tool for efficient assembly of genome-wide physical maps
BACKGROUND: Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensitive to input parameters, which describe noise inherent in the data collection proces...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965707/ https://www.ncbi.nlm.nih.gov/pubmed/27454532 http://dx.doi.org/10.1186/s12859-016-1099-1 |
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author | Sharp, Aaron R. Udall, Joshua A. |
author_facet | Sharp, Aaron R. Udall, Joshua A. |
author_sort | Sharp, Aaron R. |
collection | PubMed |
description | BACKGROUND: Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensitive to input parameters, which describe noise inherent in the data collection process. One possible way to determine the parameter values that best describe a dataset is by trial and error. RESULTS: Here we present OMWare, a tool that efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii. The assemblies were generated using various input parameter values, and were completed more efficiently by re-using compatible intermediate results. These assemblies were assayed for contiguity, internal consistency, and accuracy. CONCLUSIONS: Resulting assemblies had variable qualities. Although highly accurate assemblies were found, contiguity and internal consistency metrics were poor predictors of accuracy. |
format | Online Article Text |
id | pubmed-4965707 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-49657072016-08-02 OMWare: a tool for efficient assembly of genome-wide physical maps Sharp, Aaron R. Udall, Joshua A. BMC Bioinformatics Research BACKGROUND: Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensitive to input parameters, which describe noise inherent in the data collection process. One possible way to determine the parameter values that best describe a dataset is by trial and error. RESULTS: Here we present OMWare, a tool that efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii. The assemblies were generated using various input parameter values, and were completed more efficiently by re-using compatible intermediate results. These assemblies were assayed for contiguity, internal consistency, and accuracy. CONCLUSIONS: Resulting assemblies had variable qualities. Although highly accurate assemblies were found, contiguity and internal consistency metrics were poor predictors of accuracy. BioMed Central 2016-07-25 /pmc/articles/PMC4965707/ /pubmed/27454532 http://dx.doi.org/10.1186/s12859-016-1099-1 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Sharp, Aaron R. Udall, Joshua A. OMWare: a tool for efficient assembly of genome-wide physical maps |
title | OMWare: a tool for efficient assembly of genome-wide physical maps |
title_full | OMWare: a tool for efficient assembly of genome-wide physical maps |
title_fullStr | OMWare: a tool for efficient assembly of genome-wide physical maps |
title_full_unstemmed | OMWare: a tool for efficient assembly of genome-wide physical maps |
title_short | OMWare: a tool for efficient assembly of genome-wide physical maps |
title_sort | omware: a tool for efficient assembly of genome-wide physical maps |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965707/ https://www.ncbi.nlm.nih.gov/pubmed/27454532 http://dx.doi.org/10.1186/s12859-016-1099-1 |
work_keys_str_mv | AT sharpaaronr omwareatoolforefficientassemblyofgenomewidephysicalmaps AT udalljoshuaa omwareatoolforefficientassemblyofgenomewidephysicalmaps |