Table 1.
Comparison of Bambus Using Celera Assembler and Arachne on Five Benchmark Genomes
|
|
|
Max size |
N50 Size |
Max span |
# Errors |
|---|---|---|---|---|---|
| Brucella sius 1330 | Ca | 2,090,920 | 2,090,920 | 2,100,248 | 0 |
| CA Bambus | 1,556,915 | 1,100,469 | 1,578,082 | 0 | |
| CA Bambus norep. | 1,556,915 | 610,258 | 0 | ||
| Arachne | 1,804,830 | 1,804,830 | 1,800,825 | 0 | |
| Arachne Bambus | 1,214,328 | 511,873 | 1,217,772 | 5 | |
| Arachne Bambus norep. | 1,100,196 | 688,090 | 0 | ||
| Shewanella oneidensis MR1 | CA | 228,793 | 62,460 | 230,298 | 0 |
| CA Bambus | 228,793 | 69,276 | 231,668 | 11 | |
| CA Bambus norep. | 228,793 | 55,775 | 5 | ||
| Arachne | 244,815 | 80,523 | 251,981 | 10 | |
| Arachne Bambus | 286,184 | 81,273 | 297,842 | 26 | |
| Arachne Bambus norep. | 286,184 | 81,273 | 26 | ||
| Staphylococcus aureus COL | CA | 65,596 | 10,146 | 66,028 | 0 |
| CA Bambus | 88,011 | 15,661 | 89,215 | 18 | |
| CA Bambus norep. | 88,011 | 15,402 | 10 | ||
| Arachne | 113,689 | 18,139 | 112,139 | 7 | |
| Arachne Bambus | 113,689 | 16,614 | 114,249 | 4 | |
| Arachne Bambus norep. | 113,689 | 15,574 | 7 | ||
| Staphylococcus epidermidis RP62A | CA | 1,090,358 | 781,570 | 1,094,683 | 0 |
| CA Bambus | 776,834 | 610,961 | 791,183 | 2 | |
| CA Bambus norep. | 1,086,408 | 780,057 | 0 | ||
| Arachne | 770,082 | 734,638 | 796,757 | 0 | |
| Arachne Bambus | 1,087,230 | 768,256 | 1,141,607 | 0 | |
| Arachne Bambus norep. | 1,087,230 | 768,256 | 0 | ||
| Wolbachia spp | CA | 256,979 | 83,636 | 262,188 | 0 |
| CA Bambus | 277,395 | 117,944 | 281,045 | 0 | |
| CA Bambus norep. | 277,395 | 119,900 | 0 | ||
| Arachne | 374,494 | 255,964 | 393,785 | 0 | |
| Arachne Bambus | 376,400 | 319,924 | 383,768 | 1 | |
|
|
Arachne Bambus norep.
|
376,400
|
194,340
|
|
0
|
-
CA, Celera Assembler output; Arachne, Arachne output; CA Bambus and Arachne Bambus, Bambus scaffolds based on Celera Assembler and Arachne contigs; norep., Bambus scaffolds after repeats were masked. The first two columns indicate the maximum and N50 sizes and spans (see main text). The “# errors” column indicates the number of contigs that were incorrectly scaffolded with respect to the reference genome.
