Cargando…
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...
Autores principales: | , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2008
|
Materias: | |
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 |
_version_ | 1782155631565733888 |
---|---|
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. |
format | Text |
id | pubmed-2397507 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT phillippyadamm genomeassemblyforensicsfindingtheelusivemisassembly AT schatzmichaelc genomeassemblyforensicsfindingtheelusivemisassembly AT popmihai genomeassemblyforensicsfindingtheelusivemisassembly |