Genome assembly forensics: finding the elusive mis-assembly

We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline i...

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Detalles Bibliográficos
Autores principales: Phillippy, Adam M, Schatz, Michael C, Pop, Mihai
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397507/
https://www.ncbi.nlm.nih.gov/pubmed/18341692
http://dx.doi.org/10.1186/gb-2008-9-3-r55
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author Phillippy, Adam M
Schatz, Michael C
Pop, Mihai
author_facet Phillippy, Adam M
Schatz, Michael C
Pop, Mihai
author_sort Phillippy, Adam M
collection PubMed
description We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net.
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spelling pubmed-23975072008-05-30 Genome assembly forensics: finding the elusive mis-assembly Phillippy, Adam M Schatz, Michael C Pop, Mihai Genome Biol Software We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net. BioMed Central 2008-03-14 /pmc/articles/PMC2397507/ /pubmed/18341692 http://dx.doi.org/10.1186/gb-2008-9-3-r55 Text en Copyright © 2008 Phillippy et al.; licensee BioMed Central Ltd. https://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 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Phillippy, Adam M
Schatz, Michael C
Pop, Mihai
Genome assembly forensics: finding the elusive mis-assembly
title Genome assembly forensics: finding the elusive mis-assembly
title_full Genome assembly forensics: finding the elusive mis-assembly
title_fullStr Genome assembly forensics: finding the elusive mis-assembly
title_full_unstemmed Genome assembly forensics: finding the elusive mis-assembly
title_short Genome assembly forensics: finding the elusive mis-assembly
title_sort genome assembly forensics: finding the elusive mis-assembly
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397507/
https://www.ncbi.nlm.nih.gov/pubmed/18341692
http://dx.doi.org/10.1186/gb-2008-9-3-r55
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