Table 4

SOAPdenovo bee assembly

Assembly

Trimmed Only

Corrected

Removed

Contigs

N50

N90

Scaffolds

N50

N90

Reads


Uncorrected Corrected

146.0 M

-

12.9 M

312,414

2,383

198

90,201

37,138

9,960

167.3 M

SOAPdenovo Corrected

134.4 M

15.7 M

15.6 M

188,480

4,051

515

36,525

36,525

9,162

164.8 M

Quake

146.9 M

16.5 M

13.0 M

189,621

4,076

514

37,279

37,014

9,255

167.3 M


SOAPdenovo assemblies of Megachile rotundata 124 bp paired end reads. We trimmed the reads before correcting with SOAPdenovo, which greatly improved its performance on our experiments with simulated data. The 'Trimmed only' column includes reads trimmed before and during SOAPdenovo correction. Quake trims reads automatically during correction. Correcting the reads reduces the number of contigs and scaffolds, increases the contig sizes, and allows the assembler to include more reads. Quake corrects more reads than SOAPdenovo which results in a slightly better assembly.

Kelley et al. Genome Biology 2010 11:R116   doi:10.1186/gb-2010-11-11-r116

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