Genome assembly forensics: Finding the elusive mis-assembly

Phillippy, A. M., Schatz, M. C., Pop, M. (2008) Genome assembly forensics: Finding the elusive mis-assembly. Genome Biology, 9 (3). ISSN 14747596 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/18341692
DOI: 10.1186/gb-2008-9-3-r55

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. © 2008 Phillippy et al.; licensee BioMed Central Ltd.

Item Type: Paper
Uncontrolled Keywords: article automation bacterial genome computer program eukaryote gene rearrangement gene sequence gene structure genetic organization nonhuman nucleotide sequence validity animal artifact Bacillus anthracis DNA sequence Drosophila genetics genome methodology quality control sensitivity and specificity tandem repeat Bacteria (microorganisms) Eukaryota Animals Artifacts Sequence Analysis, DNA Software Tandem Repeat Sequences
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: Matt Covey
Date: 2008
Date Deposited: 15 Mar 2013 16:52
Last Modified: 15 Mar 2013 16:52
PMCID: PMC2397507
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27829

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