Table 5.
Assembly statistics
| Assembler | Sequencing | Strains | Insert size | Read length (bp) | Number of reads | Raw read coverage | Assembled bases (Mb) | Contig coverage | Contig N50 |
|---|---|---|---|---|---|---|---|---|---|
| FuzzyPath | Illumina | CAST/Ei | 200 bp | 36 | 173 million | 65× | 76.03 | 80.0% | 2,315 |
| Velvet* | Illumina | CAST/Ei | 200 bp | 36 | 173 million | 65× | 58.09 | 61.15% | 391 |
| ABySS | Illumina | CAST/Ei | 200 bp | 36 | 173 million | 65× | 72.80 | 76.63% | 1,022 |
| FuzzyPath | Illumina | A/J | 200 bp | 36 | 112 million | 42× | 55.87 | 58.8% | 959 |
| Phusion | Capillary | A/J | 3-5 kb | 400-900 | 357,100 | 2.5× | 81.2 | 85.5% | 3,377 |
| FuzzyPath | Hybrid | A/J† | Hybrid† | Hybrid† | Hybrid† | Hybrid† | 85.54 | 90.0% | 5,793 |
*Version 0.4. We also tried the latest version 0.7, which had been much improved in terms of contig length, but ran out of memory on a computer with 192 Gb RAM. †Assembly incorporating the A/J Illumina reads and Celera capillary reads.