Table 1.
Assembly statistics of Velvet applied on Staphylococcus aureus (MRSA) strain E-MRSA15-CC22-SCC mec IV showing an increase in contig size and N50 when using higher k-mer sizes, but revealing a mis-assembly starting from k-mer size 97 using whole genome mapping
| K-mer size | N50 | Total number of contigs | Longest contig size | Mis-assemblies on mapped contigs* | Approx. nts involved in mis-assemblies |
|---|---|---|---|---|---|
|
Velvet |
|
||||
| 81 |
162295 |
40 |
340060 |
1 (10) |
122303 |
| 83 |
170447 |
38 |
351373 |
1 (9) |
122303 |
| 85 |
170449 |
37 |
351321 |
0 (10) |
|
| 87 |
173763 |
33 |
351326 |
0 (10) |
|
| 89 |
173765 |
33 |
351394 |
0 (10) |
|
| 91 |
173767 |
33 |
351330 |
0 (10) |
|
| 93 |
173769 |
35 |
340092 |
0 (10) |
|
| 97 |
175770 |
33 |
365247 |
1 (9) |
130273 |
| 99 |
175776 |
33 |
365260 |
1 (10) |
130273 |
| 101 |
187438 |
32 |
365623 |
1 (9) |
130273 |
| 103 |
187448 |
32 |
365625 |
1 (9) |
130273 |
| 105 |
187458 |
32 |
365638 |
1 (9) |
130273 |
| 107 |
187465 |
33 |
365647 |
1 (9) |
130273 |
| 109 |
212189 |
32 |
365656 |
1 (9) |
130273 |
| 111 |
212287 |
33 |
349286 |
2 (8) |
93632 & 153207 |
| 113 |
212292 |
34 |
349288 |
1 (10) |
93634 |
| 115 |
212294 |
34 |
349290 |
1 (10) |
118928 |
| 117 |
174074 |
35 |
349419 |
1 (11) |
93634 |
| 119 |
174076 |
35 |
349423 |
1 (11) |
93638 |
| 121 |
170642 |
37 |
349435 |
0 (11) |
|
| 123 | 170654 | 38 | 340456 | 0 (10) | |
*Number of mapped contigs indicated between brackets.