Table 2

The human chromosome 14 assembly results in terms of continuity, accuracy, and statistics.

Evaluations

Continuity

Accuracy

Statistics


Contig #

NG50 (kbp)

NG50 corr. (kbp)

SNP

Indels

Misjoins

Asm. (%)

Unaligned ref. (%)

Duplicated ref. (%)


Velvet 61k

28,974

5.2

4.7

82,235

17,755

601

96.69

2.09

0.43


Tiger-Velvet-R 125i

20,189

11.6

9.3

84,577

21,847

533

97.90

1.98

1.50


Tiger-Velvet-I 7i

21,623

10.9

8.9

84,811

21,470

654

98.43

1.53

1.48


SOAPdenovo 55k

50,094

3.0

3.0

67,956

11,866

36

95.91

3.13

0.28


Tiger-Soap-R 120i

60,134

3.6

3.4

68,881

12,839

185

99.40

3.01

2.79


Tiger-Soap-I 7i

55,173

3.8

3.6

69,215

13,390

205

98.68

2.43

1.46


The columns include the number of contigs, NG50 size and its error-corrected size, the number of single nucleotide polymorphisms (SNPs), the number of indels and misjoins in contigs, total assembly length, genome coverage (100 - Unaligned ref.), and duplications. K-mer 61 and 55 are the best k-mer sizes for Velvet and SOAPdenovo, respectively. "#k" stands for the applied k-mer size. "#i" stands for the iteration number.

Wu et al. BMC Bioinformatics 2012 13(Suppl 19):S18   doi:10.1186/1471-2105-13-S19-S18

Open Data