The emergence of next-generation sequencing platforms has made low-cost sequencing an attractive approach for de novo assembly of genomes and transcriptomes. The two most widely used next-generation platforms for de novo assembly are the Illumina and Roche 454, and each system has particular strengths and weaknesses.

The Illumina generates short reads (100 bp) while the Roche 454 FLX+ produces read lengths close to Sanger (800 bp). However, the price per base on the Roche 454 machine is approximately 50x higher than on the Illumina platform. Few studies exist which employ assembly of both read types [1, 2], and the methods used are not explicitly described.

If there was a way to assemble data from both platforms, researchers could capitalize on the strengths of each system while minimizing the weaknesses and cost. To this end, we evaluated multiple strategies for combined Illumina and Roche 454 de novo assembly, using sequencing data from several genomes and transcriptomes of varying size and origin.

From our research, we developed methods to consolidate these two sequencing technologies, resulting in assemblies that perform better than those using any individual sequencing technology alone. Our analysis shows that the merger of separate assemblies of Roche 454 reads and Illumina raw reads produces the best assembly metrics for genomes < 10 Mb and for transcriptomes. Yet for genomes > 10Mb, assembling Illumina raw reads with Roche 454 assembled fragments, produces similar results. In this poster we presented at AGBT, we describe our findings on various data sets as well as report the types of assemblers used and workflows specific to genome and transcriptome assemblies.

Bottom line: a multi-platform approach can significantly increase assembly contiguity for both genome and transcriptome assemblies.

1.  Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 2009 February; 19(2): 294–305.

2.  Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet. 2010 Apr 8;6(4):e1000891.