Table 3

E. coli (SRR001665) 24-tile assembly results in terms of contiguity, accuracy, and statistics.

Evaluations

Continuity

Accuracy

Statistics


Contig #

NG50 (kbp)

NG50 corr. (kbp)

SNP

Indels

Misjoins

Asm. (%)

Unaligned ref. (%)

Duplicated ref. (%)


Velvet 25k

147

87.0

67.3

238

37

2

97.89

0.56

0.01


Tiger-Velvet-R 51i

281

95.6

87.2

190

35

3

100.92

0.14

2.30


Tiger-Velvet-I 7i

276

95.4

87.2

211

33

12

100.40

0.12

1.68


SOAPdenovo 27k

450

17.9

17.9

12

4

1

97.56

1.31

0.00


Tiger-Soap-R 80i

524

25.6

25.6

31

11

3

98.67

1.20

0.78


Tiger-Soap-I 7i

509

25.8

25.8

23

6

2

98.78

0.80

0.64


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 25 and 27 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. Both Tiger-Velvet-I and Tiger-Soap-I evaluations use the best results from Velvet and SOAPdenovo as input, respectively.

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

Open Data