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

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

Name of Assembly	Assembler	CM334			Maor			Early Jalapeño (EJ)
		No. of Contigs^a	N50	Total Assembled nt.	No. of Contigs^a	N50	Total Assembled nt.	No. of Contigs^a	N50	Total Assembled nt.
Super Assembly	Velvet^b	75,853	1,287	71,903,681	70,459	1,303	67,210,074	81,973	1,198	73,865,962
	CLC^c	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

^a No of contigs longer than 300 nucleotides were included in all assemblies.
^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.
^c Two CLC iterations including one normally trimmed data and one stringently trimmed data were assembled using CAP3 program.

ISSN: 1471-2164