Skip to main content

Advertisement

Table 1 Results and characteristics of assemblies run with different parameter settings.

From: Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

   Gap Penalty
   30 50
Match % Match length Number of contigs and average length Number of assembled reads Number of contigs and average length Number of assembled reads
85% 19 50,689 (537) 255,711 51,058 (533) 252,299
  23 49,621 (516) 248,537 50,039 (513) 245,563
  25 48,962 (507) 244,120 49,366 (504) 241,289
90% 19 55,886 (499) 220,517 55,996 (497) 217,169
  23 53,724 (490) 213,344 53,824 (488) 209,916
  25 52,770 (485) 209,735 52,726 (483) 206,167
95% 19 51,289 (443) 156,578 51,908 (441) 154,605
  23 46,611 (441) 142,428 46,585 (439) 140,071
  25 44,752 (439) 137,096 44,674 (437) 134,566
Combination of reference-based (match % = 88) and de novo assemblies (match % = 93)
88%,93% 19 63,687 (500) 225,517   
  1. Results from assemblies run in Seqman Ngen with different starting values for gap penalty, minimum match size, and mimimum match percentage. We present the number of contigs, average contig size (in parentheses), and the number of reads assembled into contigs for each different set of parameter settings.