Table of Contents
Volume 2010, Article ID 782465, 12 pages
Research Article

Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads

Department of Biology, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway

Received 26 May 2009; Revised 28 September 2009; Accepted 5 November 2009

Academic Editor: Nick Loman

Copyright © 2010 Alexander J. Nederbragt et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with a number of contigs having a depth that is far higher than can be expected. For reference genome sequence datasets, there exists a high correlation between the contig specific read depth and the number of copies present in the genome. We developed a sequence of applied statistical analyses, which suggest that the number of copies present can be reliably estimated based on the read depth distribution in de novo genome assemblies. Read depths of contigs of de novo cyanobacterial genome assemblies were determined, and several high read depth contigs were identified. These contigs were shown to mainly contain genes that are known to be present in multiple copies in bacterial genomes. For these assemblies, a correlation between read depth and copy number was experimentally demonstrated using real-time PCR. Copy number estimates, obtained using the statistical analysis developed in this work, are presented. Per-contig read depth analysis of assemblies based on 454 reads therefore enables de novo detection of genomic repeats and estimation of the copy number of these repeats. Additionally, our analysis efficiently identified contigs stemming from sample contamination, allowing for their removal from the assembly.