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

BMC Genomics

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

		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

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.

ISSN: 1471-2164