Table 2.
Selected quality indicators for the best genome assembly of B. fragilis CCUG4856T per assembly pipeline
RefSeq accession GCF_000025985.1 was used as a reference. CM, Canu-corrected with option corMinCoverage=0; CO, Canu-corrected with option coroutCoverage=999; CS, Canu-corrected standard settings; OF, ONT reads filtered with Filtlong; PI[n], Pilon polishing with Illumina reads, [n] rounds; RI, Racon polishing with Illumina reads; RO2, two rounds of Racon polishing with ONT reads. Full results are available in Table S2.
|
Assembly |
No. of contigs |
Largest contig |
Total length |
Mis-assemblies |
Genome fraction (%) |
Mismatches per 100 kbp |
Indels per 100 kbp |
ANI |
CheckM completeness |
busco score: complete and single-copy/ complete and duplicate/ fragment (of 443) |
Prokka genes |
Prokka rRNA |
Prokka tRNA |
Total ale score |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GCF_000025985.1 |
2 |
5 205 140 |
5 241 700 |
0 |
100.000 |
0 |
0 |
100.000 |
99.26 |
442/0/1 |
4439 |
19 |
73 |
−17071758.95 |
|
Skesa |
46 |
553 341 |
5 201 945 |
3 |
99.237 |
0.23 |
0.15 |
99.998 |
99.26 |
440/2/1 |
4391 |
2 |
62 |
−20926329.69 |
|
SPAdes |
23 |
1 779 941 |
5 212 217 |
4 |
99.396 |
0.44 |
0.17 |
99.987 |
99.26 |
440/2/1 |
4407 |
3 |
56 |
−19676529.39 |
|
Canu.OF.CO.RO2.RI.PI3 |
2 |
5 247 938 |
5 350 432 |
8 |
99.972 |
4.94 |
15.9 |
99.975 |
99.26 |
442/0/1 |
4634 |
19 |
73 |
−19283611.73 |
|
Flye.OF.CS.PI5.RI |
5 |
2 282 650 |
5 269 269 |
4 |
99.917 |
1.07 |
6.24 |
99.978 |
99.26 |
441/1/1 |
4476 |
19 |
73 |
−18222322.23 |
|
Miniasm.OF.CM.RO2.PI5 |
3 |
5 204 445 |
5 277 434 |
2 |
99.972 |
5.21 |
17.75 |
99.969 |
98.88 |
442/0/1 |
4607 |
19 |
73 |
−17789234.97 |
|
Wtdbg2.OF.CO.RO2.PI6.RI |
3 |
5 192 352 |
5 234 448 |
7 |
99.723 |
3.23 |
3.04 |
99.981 |
99.26 |
442/0/1 |
4437 |
19 |
73 |
−18750266.21 |
|
SPAdesHybrid.CS |
5 |
3 093 122 |
5 242 724 |
7 |
99.987 |
1.89 |
0.53 |
99.986 |
99.26 |
440/2/1 |
4441 |
19 |
73 |
−18535980.68 |
|
Unicycler.OF.CS |
2 |
5 205 133 |
5 241 693 |
2 |
99.972 |
0.84 |
0.48 |
100.000 |
99.26 |
442/0/1 |
4435 |
19 |
73 |
−17200232.52 |