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|
Org.
|
X
|
Tool
|
Compl. [%]
|
#ctg
|
#MA
|
MM
|
InDels
|
NA50
|
|---|
|
Yeast
|
\({\sim} 5\times \)
|
LazyB
|
90.466
|
127
|
9
|
192.56
|
274.62
|
118843
|
|
LazyB+QM
|
94.378
|
64
|
12
|
174.77
|
245.05
|
311094
|
|
Canu
|
14.245
|
115
|
5
|
361.47
|
2039.15
|
–
|
|
Wtdbg2
|
22.237
|
177
|
0
|
849.07
|
805.31
|
–
|
|
HASLR
|
64.158
|
111
|
1
|
14.87
|
34.86
|
60316
|
|
DBG2OLC
|
45.645
|
53
|
20
|
2066.64
|
1655.92
|
–
|
|
Wengan
|
95.718
|
41
|
11
|
49.14
|
68.47
|
438928
|
|
\({\sim} 11\times \)
|
LazyB
|
97.632
|
33
|
15
|
193.73
|
300.20
|
505126
|
|
LazyB+QM
|
94.211
|
34
|
14
|
234.59
|
329.4
|
453273
|
|
Canu
|
92.615
|
66
|
15
|
107.00
|
1343.37
|
247477
|
|
Wtdbg2
|
94.444
|
42
|
8
|
420.96
|
1895.28
|
389196
|
|
HASLR
|
92.480
|
57
|
1
|
7.89
|
33.91
|
251119
|
|
DBG2OLC
|
97.689
|
38
|
25
|
55.06
|
1020.48
|
506907
|
|
Wengan
|
96.036
|
37
|
4
|
32.35
|
53.04
|
496058
|
|
\({\sim} 80\times \)
|
Abyss
|
95.247
|
283
|
0
|
9.13
|
1.90
|
90927
|
|
Fruit fly
|
\({\sim} 5\times \)
|
LazyB
|
71.624
|
1879
|
68
|
446.19
|
492.43
|
64415
|
|
LazyB+QM
|
75.768
|
1164
|
79
|
322.49
|
349.29
|
167975
|
|
Canu
|
–
|
–
|
–
|
–
|
–
|
–
|
|
Wtdbg2
|
6.351
|
2293
|
2
|
916.77
|
588.19
|
–
|
|
HASLR
|
24.484
|
1407
|
10
|
31.07
|
58.96
|
–
|
|
DBG2OLC
|
25.262
|
974
|
141
|
1862.85
|
969.26
|
–
|
|
Wengan
|
81.02
|
2129
|
192
|
105.35
|
123.33
|
77215
|
|
\({\sim} 10\times \)
|
LazyB
|
80.111
|
596
|
99
|
433.37
|
486.28
|
454664
|
|
LazyB+QM
|
80.036
|
547
|
100
|
416.34
|
467.14
|
485509
|
|
Canu
|
49.262
|
1411
|
275
|
494.66
|
1691.11
|
–
|
|
Wtdbg2
|
41.82
|
1277
|
155
|
2225.12
|
1874.01
|
–
|
|
HASLR
|
67.059
|
2463
|
45
|
43.83
|
84.89
|
36979
|
|
DBG2OLC
|
82.52
|
487
|
468
|
739.47
|
1536.32
|
498732
|
|
Wengan
|
84.129
|
926
|
237
|
114.96
|
154.03
|
221730
|
|
\({\sim} 45\times \)
|
Abyss
|
83.628
|
5811
|
123
|
6.20
|
8.31
|
67970
|
|
Human
|
\({\sim} 10\times \)
|
LazyB
|
67.108
|
13210
|
2915
|
1177.59
|
1112.84
|
168170
|
|
\({\sim} 43\times \)
|
Unitig
|
69.422
|
4146090
|
252
|
93.07
|
13.65
|
338
|
|
\({\sim} 43\times \)
|
Abyss
|
84.180
|
510315
|
2669
|
98.53
|
25.03
|
7963
|
- LazyB outperforms Canu and Wtdbg2 in all categories, while significantly reducing contig counts compared to short-read only assemblies. While HASLR is more accurate, it covers significantly lower fractions of genomes at a higher contig count and drastically lower NA50. DBG2OL produces few contigs at a high NA50 for higher coverage cases, but calls significantly more mis-assemblies. Wengan performs well for yeast, but produces more misassemblies at a higher contig count on fruit fly. Merging LazyB assemblies to the set of short read contigs (+QM) has a positive effect at 5\(\times \) long-read coverage but negligible influence at higher coverage. Mismatches and InDels are given per 100 kb. Accordingly, errors in LazyB ’s unpolished output constitute \(<1\)% except for human. Wtdbg2 assemblies were not polished. Column descriptions: X coverage of sequencing data, completeness of the assembly. #ctg: number of contigs, #MA: number of mis-assemblies (breakpoints relative to the reference assembly) M is Matches and InDels relative to the reference genomes. NA50 of correctly assembled contigs. We follow the definition of QUAST: Given a set of fragments as the sub-regions of the original contigs that were correctly aligned to the reference, the NA50 (also named NGA50) is defined as the minimal length of a fragment needed to cover 50% of the genome. This value is omitted when \(< 50\%\) is correctly recalled
