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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.