Table 2

Forge assemblies

ID

454

Sanger-454

Sanger-454-IlluminaPA

Sanger-454-IlluminaDA


Total scaffolds*

7,860

4,805

2,307

1,443

N50 contig (scaffold)

5,773 (N/A)

7,440 (289,760)

31,821 (557,565)

164,278 (187,326)

Total DNA (bp)

29,484,877

34,841,371

39,238,044

29,522,629

Number of scaffolds with gaps

0

656

163

17

Augustus predictions

10,555

10,230

8,912

8,476

EST analysis§

5,544/25

5,747/60

6,314/40

6,685/33


*Scaffolds included in this calculation contained two or more reads and were longer than 500 bp. Total DNA was calculated excluding gaps and was performed on scaffolds that contained two or more reads and were longer than 500 bp. Gaps included in this calculation were longer than 50 bp. §EST alignments are given as: Complete alignments/Misassemblies (see Materials and methods). Forge assemblies were generated using Illumina, 454 and Sanger read data. The '454' assembly was generated using only 454 SE read data. The 'Sanger-454' assembly was generated by combining the Sanger PE and 454 SE read collections. The 'Sanger-454-IlluminaPA' assembly was generated by combining the Sanger PE and 454 SE read collections with preassembled (PA) contigs generated from Illumina PE reads with Velvet. The 'Sanger-454-IlluminaDA' assembly was generated by combining the Sanger PE and 454 SE read collections with Illumina PE reads (DA = direct assembly).

DiGuistini et al. Genome Biology 2009 10:R94   doi:10.1186/gb-2009-10-9-r94

Open Data