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Table 2 Forge assemblies

From: De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

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
  1. *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).