Genome assembly quality: assessment and improvement using the neutral indel model.

Genome Res. 2010 May;20(5):675-84. Epub 2010 Mar 19.


We describe a statistical and comparative-genomic approach for quantifying error rates of genome sequence assemblies. The method exploits not substitutions but the pattern of insertions and deletions (indels) in genome-scale alignments for closely related species. Using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters of nucleotides that were wrongly inserted or deleted during sequencing or assembly.


Meader S, Hillier LW, Locke D, Ponting CP, Lunter G.

Institute Authors

LaDeana Hillier