Skip to main content

Table 4 Summary statistics of transcriptome assembly of three pepper lines using Velvet, CLC and CAP3 assemblers

From: De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

Name of Assembly Assembler CM334 Maor Early Jalapeño (EJ)
   No. of Contigsa N50 Total Assembled nt. No. of Contigsa N50 Total Assembled nt. No. of Contigsa N50 Total Assembled nt.
Super Assembly Velvetb 75,853 1,287 71,903,681 70,459 1,303 67,210,074 81,973 1,198 73,865,962
  CLCc 83,187 1,357 79,564,926 76,542 1,389 74,367,265 81,528 1,347 78,144,374
Mega Assembly CAP3 83,113 1,488 84,792,180 76,375 1,526 79,383,673 82,614 1,488 84,973,865
(Velvet+CLC) Combined CM334, Maor, EJ
Meta Assembly (3 lines) CAP3        123,261 1,647 135,019,787
  1. a No of contigs longer than 300 nucleotides were included in all assemblies.
  2. b Six Velvet iterations including three k-mers of normally trimmed data and 3 k-mers of stringently trimmed data were assembled using CAP3 program.
  3. c Two CLC iterations including one normally trimmed data and one stringently trimmed data were assembled using CAP3 program.