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Table 2 Comparison of de novo assemblies used in this study

From: A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

Assembly Trinity CLC-GWB Velvet/OASES SOAPdenovo-Trans Final assembly
# contigs (> = 0 bp) 431,255 508,239 798,345 289,705 906,566
# contigs (> = 1000 bp) 210,220 109,992 37,698 34,781 294,867
# contigs (> = 2000 bp) 104,013 34,970 2,633 4,817 130,095
# contigs (> = 3000 bp) 46,942 13,732 441 1,099 57,437
# contigs (> = 4000 bp) 19,218 5,574 94 282 23,416
# contigs (> = 5000 bp) 7,542 2,413 31 104 9,227
# contigs 431,255 508,239 798,345 289,705 906,566
Largest contig 28,461 29,928 11,272 18,497 9,990
Total length 608,060,518 419,587,279 409,817,309 182,675,172 966,867,516
GC (%) 43.88 43.50 42.84 43.25 43.67
N50 2,194 1,014 516 674 1,671
N75 1,216 542 389 455 745
L50 89,618 107,715 266,636 82,953 168,723
L75 181,071 253,430 497,065 165,967 385,929
# N’s per 100 kbp 0 0 0 0 0