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 webcite

* Illumina technology - [26]http://www.sanger.ac.uk webcite; 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.

Samarakoon et al. BMC Genomics 2011 12:116   doi:10.1186/1471-2164-12-116

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