Table 2

Genome assembly statistics and summary
Genome Step Software Size a # contigs b # scaffolds Average length c N50 d N90 e
Tcm 454 assembly CELERA 37.3 30,737 - 1,216 1,670 539
Illumina assembly Velvet (kmer 43) 16.7 9,247 - 1,813 2,378 851
Assembly of non-assembled Illumina reads Velvet (kmer 53) 1.17 2,094 - 562 536 418
Assembly merging Zorro 33.5 24,799 f - 1,353 2,218 549
Scaffolding SSPACE 38.8 23,813 f 1,835 2,296 25,044 576
Gap closure IMAGE 38.6 23,000 1,774 2,302 25,781 583
Tcc X10 454 assembly CELERA 41.8 33,686 - 1,243 1,516 549
Illumina assembly Velvet (kmer 43) 17.0 8,523 - 1,997 2,742 904
Assembly of non-assembled Illumina reads Velvet (kmer 53) 1.14 2,116 - 543 523 416
Assembly merging Zorro 38.0 28,389 f - 1,339 1,869 560
Scaffolding SSPACE 43.7 27,605 f 2,476 2,162 14,067 589
Gap closure IMAGE 43.4 26,889 2,423 2,158 14,516 592

a The length when sequences are combined (Mb).

b The number of contigs/scaffolds.

c The average contig length (bp). For the SSPACE row, this refers to the average scaffold length.

d The length N for which half of all bases are in a sequence of this length or longer.

e The length N for which 90% of all bases are in a sequence of this length or longer.

f Contigs >500 bp.

Franzén et al.

Franzén et al. BMC Genomics 2012 13:531   doi:10.1186/1471-2164-13-531

Open Data