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Table 3 The effect of trimming the reads and k-mer length on the number of contigs and N50 in IGA transcriptome assembly

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

Type of Reads/k-mer value* CM334 Maor Early Jalapeño
  Total No. of Contigs No. Contigs >1 KB Percent Contigs > 1 KB N50 Total No. of Contigs No. Contigs > 1 KB Percent Contigs > 1 KB N50 Total No. of Contigs No. Contigs > 1 KB Percent Contigs > 1 KB N50
Untrimmed/K31 65,337 52,179 80 603 62,570 50,306 80 589 68,737 57,077 83 497
Untrimmed/K35 64,096 49,875 78 680 61,561 48,345 79 660 68,237 55,564 81 562
Untrimmed/K41 52,099 36,770 71 947 50,290 35,900 71 926 58,431 44,045 75 777
Trimmed 25–70/K31 42,310 30,628 72 864 36,173 24,871 69 995 39,956 28,711 72 870
Trimmed 25–70/K35 34,525 22,627 66 1,109 30,202 18,859 62 1,205 34,497 23,039 67 1,057
Trimmed 25–70/K41 27,439 16,728 61 1,239 26,885 16,660 62 1223 28,588 18,162 64 1,165
  1. * The untrimmed reads were between 40–80 nt long. The same reads were trimmed by 5 and 10 nt from 5' an 3' ends respectively to eliminate the possible sequencing errors at the beginning and at the end of each read. The numbers were selected arbitrarily but K=31 is the Velvet recommended value.