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. 2008 Sep;18(9):1538-43.
doi: 10.1101/gr.076067.108. Epub 2008 Jun 11.

EagleView: a genome assembly viewer for next-generation sequencing technologies

Weichun Huang  1 , Gabor Marth
Affiliations

EagleView: a genome assembly viewer for next-generation sequencing technologies

Weichun Huang et al. Genome Res. 2008 Sep.

Abstract

The emergence of high-throughput next-generation sequencing technologies (e.g., 454 Life Sciences [Roche], Illumina sequencing [formerly Solexa sequencing]) has dramatically sped up whole-genome de novo sequencing and resequencing. While the low cost of these sequencing technologies provides an unparalleled opportunity for genome-wide polymorphism discovery, the analysis of the new data types and huge data volume poses formidable informatics challenges for base calling, read alignment and genome assembly, polymorphism detection, as well as data visualization. We introduce a new data integration and visualization tool EagleView to facilitate data analyses, visual validation, and hypothesis generation. EagleView can handle a large genome assembly of millions of reads. It supports a compact assembly view, multiple navigation modes, and a pinpoint view of technology-specific trace information. Moreover, EagleView supports viewing coassembly of mixed-type reads from different technologies and supports integrating genome feature annotations into genome assemblies. EagleView has been used in our own lab and by over 100 research labs worldwide for next-generation sequence analyses. The EagleView software is freely available for not-for-profit use at http://bioinformatics.bc.edu/marthlab/EagleView.

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Figures

Figure 1.
Figure 1.
Illustration of EagleView features. The EagleView shown in the figure is the version for Microsoft Windows. All features except the mouse-tip window shown in the figure are also available for both Linux and Mac versions. The upper part shows a genome assembly of 454 sequence reads; the lower part displays an assembly of Illumina reads.
Figure 2.
Figure 2.
The genome assembly of human chromosome Y with real SNP position map. (A) A single SNP site with ID rs1053790, heterozygote frequency (HF) 0.26, and dbSNP validation status (VS) 2 (at least one sub-SNP in cluster has frequency data submitted). (B) A region with high density of SNPs. At the SNP site at position 57,440,427, the sequence error and alignment error potentially contribute wrong genotype A/C/G called at the position where the true genotype is C/G. (C) A deletion under the SNP site is due to an alignment error.
Figure 3.
Figure 3.
Two examples of SNP genotype discrepancies between the HapMap project and the new assembly data from the 1000 Genomes Project. In the figure, the HapMap SNP ID and genotypes are shown in the white and bold font. In the left panel, the assembly shows a rare allele C in the position not reported in the HapMap. In the right panel, the assembly shows a deletion SNP but HapMap reports that it is A/T SNP. The deletion SNP likely to be true as Illumina sequencing technology has a very low rate of insertion/deletion sequencing errors.
See this image and copyright information in PMC

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