Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application
Table 2
Evaluation of dnaasm-link application in comparison to other tools for datasets depicted in Table 1. The first row in table, where algorithm name is “no scaffolding”, provides the input set statistics (no scaffolding algorithm is used) taken from Table 1. The parameters (No. of contigs, etc.) are depicted in first paragraph of “Results” section.
No. of contigs
No. of mis.
N50 [bp]
NA50 [bp]
Max [bp]
Largest algn. [bp]
Avg. mis.
Avg. indels
Avg. N’s
E. coli
no scaffolding
65
9
176396
164044
398301
360084
2.32
0.17
0.00
SSPACE-LongRead
32
29
398301
211043
1274776
564486
2.47
0.37
570.90
LINKS
23
19
637611
235726
1146701
636452
2.36
0.39
233.43
dnaasm-link
22
20
746714
219242
1128693
636452
2.36
0.37
212.75
Fast-SG + OPERA-LG
26
16
349966
342146
659623
658295
2.36
0.30
326.53
Fast-SG + BOSS
60
14
177523
164044
611106
360084
2.32
0.17
64.79
Fast-SG + ScaffMatch
55
18
185955
177523
603113
359089
2.41
0.17
139.44
S. cerevisiae
no scaffolding
430
53
53444
49075
257346
249232
85.77
8.80
0.00
SSPACE-LongRead
557
105
167867
126607
736874
452023
95.42
11.27
3690.74
LINKS
202
89
202618
126598
623140
416048
87.04
10.00
850.77
dnaasm-link
190
92
224004
126353
764024
431875
87.28
10.08
861.19
Fast-SG + OPERA-LG
202
59
180866
155226
736942
451889
85.51
9.72
462.50
Fast-SG + BOSS
369
113
57097
47994
257346
249232
85.77
8.80
374.16
Fast-SG + ScaffMatch
328
144
80833
51157
434320
249232
85.41
8.82
489.70
The following reference sequences were used to evaluate the results: NC_000913 for E. coli and NC_001133 … NC_001148, NC_001224 for S. cerevisiae.
