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PMID: 18341692 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Genome assembly forensics: finding the elusive mis-assembly.

Genome biology ·Vol. 9 ·No. 3 ·2008-00-00 ·Pages R55

Phillippy AM, Schatz MC, Pop M

Abstract

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.

MeSH Terms
Animals Artifacts Bacillus anthracis/genetics Drosophila/genetics Genome Quality Control Sensitivity and Specificity Sequence Analysis, DNA/methods Software Tandem Repeat Sequences
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Phillippy Adam M
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. amp@umiacs.umd.edu
Schatz Michael C
Pop Mihai
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2008-9-3-r55
Email
amp@umiacs.umd.edu
Published
2008-00-00
Epub
2008-00-14
Pages
R55
Language
English
Region
England
NLM ID
100960660
PMCID
PMC2397507
Subset
IM
Grants
NLM NIH HHS · R01 LM006845 · United States
NLM NIH HHS · R01 LM007938 · United States
NLM NIH HHS · R01-LM007938 · United States
NLM NIH HHS · R01-LM06845 · United States
External Links
PubMed source DOI: 10.1186/gb-2008-9-3-r55 PMC Full Text View journal details
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