Table 9 Assembly statistics for clustering and random splitting of a real sample
From: Centroid based clustering of high throughput sequencing reads based on n-mer counts
Splitting | Mapped reads | Total bp in contigs | Number of contigs | n50 |
|---|---|---|---|---|
Velvet assembly, hash length 21 | ||||
All reads | 1507427 (6.99%) | 470740477 | 5650689 | 79 |
Soft EM, 2 clusters | 1555663 (7.21%) | 492995773 | 5928907 | 52 |
EM, 2 clusters | 1458627 (6.76%) | 453165323 | 5454404 | 65 |
k-means, 2 clusters | 1475586 (6.84%) | 455384651 | 5474129 | 124 |
GC content, 2 parts | 1455825 (6.75%) | 451987554 | 5437853 | 70 |
Random splitting, 2 clusters | 1259894 (5.84%) | 428174983 | 5219268 | 94 |
Soft EM, 3 clusters | 1614090 (7.48%) | 528221487 | 6359119 | 78 |
EM, 3 clusters | 1429190 (6.63%) | 443042444 | 5343548 | 55 |
k-means, 3 clusters | 1439961 (6.68%) | 443713631 | 5347679 | 77 |
GC content, 3 parts | 1397108 (6.48%) | 436515238 | 5278594 | 98 |
Random splitting, 3 clusters | 1036477 (4.81%) | 392638398 | 4878611 | 48 |
Velvet assembly, hash length 31 | ||||
All reads | 2327126 (10.79%) | 290798616 | 2578825 | 100 |
Soft EM, 2 clusters | 2263596 (10.50%) | 292536888 | 2643061 | 204 |
EM, 2 clusters | 2112597 (9.79%) | 266185624 | 2412045 | 126 |
k-means, 2 clusters | 2129306 (9.87%) | 267875650 | 2424380 | 86 |
GC content, 2 parts | 2106489 (9.77%) | 265677735 | 2407873 | 100 |
Random splitting, 2 clusters | 1629402 (7.55%) | 222061071 | 2101527 | 104 |
Soft EM, 3 clusters | 2269196 (10.52%) | 310107203 | 2839376 | 226 |
EM, 3 clusters | 2002261 (9.28%) | 255782318 | 2354233 | 86 |
k-means, 3 clusters | 2006030 (9.30%) | 256111968 | 2358231 | 114 |
GC content, 3 parts | 1934436 (8.97%) | 247356556 | 2283296 | 106 |
Random splitting, 3 clusters | 1257062 (5.83%) | 184143812 | 1807765 | 141 |
Velvet assembly, hash length 41 | ||||
All reads | 1403308 (6.51%) | 118746013 | 848180 | 127 |
Soft EM, 2 clusters | 1289123 (5.98%) | 110992860 | 805140 | 188 |
EM, 2 clusters | 1182223 (5.48%) | 99860264 | 725769 | 129 |
k-means, 2 clusters | 1191102 (5.52%) | 100436034 | 728680 | 125 |
GC content, 2 parts | 1182618 (5.48%) | 100638247 | 733416 | 127 |
Random splitting, 2 clusters | 839681 (3.89%) | 73260257 | 558661 | 83 |
Soft EM, 3 clusters | 1275142 (5.91%) | 114111918 | 836929 | 156 |
EM, 3 clusters | 1081154 (5.01%) | 92510990 | 683516 | 169 |
k-means, 3 clusters | 1078651 (5.00%) | 92021168 | 679148 | 136 |
GC content, 3 parts | 1027385 (4.76%) | 86928363 | 641027 | 136 |
Random splitting, 3 clusters | 622242 (2.88%) | 55079268 | 435757 | 149 |