Table 2.
Comparison of de novo assembly between 454 GS FLX, Sanger and Illumina platforms.
| 454 pyrosequencing | Sanger sequencing^ | Illumina sequencing* | ||||
| Progeny | Parents | Reference genome | ||||
| 7C126 | SC05 | Dd2 | HB3 | NP-3D7-S | NP-3D7-L | |
| Number of Scaffolds | 970 | 2,349 | 2,837 | 1,189 | NA | NA |
| N50 Scaffold Size (kb) | 35.5 | 11.1 | 19.11 | 96.5 | NA | NA |
| Number of Contigs | 9,452 | 9,597 | 4,511 | 2,971 | 26,920 | 22,839 |
| N50 Contig Size (kb) | 3.3 | 3.3 | 11.61 | 20.62 | 1.5 | 1.6 |
| Largest Contig (kb) | 36.7 | 34.4 | NA | NA | NA | NA |
| Number of assembled bases (Mb) | 20.8 | 21.1 | 19.5 | 23.4 | 19.02 | 21.09 |
| Average Coverage | 33× | 36× | 7.8× | 7.1× | 43× | 64× |
^ Sanger technology - [50], http://www.broadinstitute.org
* Illumina technology - [26]http://www.sanger.ac.uk; NP:No-PCR libraries; Suffixes L and S indicate long and short sequencing runs performed from the same library
We compared the de novo assembly results from 454 GS FLX platform with the parental genome assembly information obtained using conventional Sanger technology, and 3D7 resequencing assembly information using the Illumina platform.