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 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.
Phillippy
Adam M
AM
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. amp@umiacs.umd.edu
Schatz
Michael C
MC
Pop
Mihai
M
D000818:Animals; D016477:Artifacts; D001408:Bacillus anthracis / Q000235:genetics; D004330:Drosophila / Q000235:genetics; D016678:Genome; D011786:Quality Control; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020080:Tandem Repeat Sequences