Table 2 Assemblies using SIMBA
From: SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
Genome | NGS | Software | Contigs | Scaffolding method | Genome length (bp) | Total scaffolds | Reference |
|---|---|---|---|---|---|---|---|
Corynebacterium pseudotuberculosis 258 (Cp258) | Ion PGM | Mira3 | 41 | Optical mapping (enzyme kpnI) | 2,369,817 | 15 | Data not published. |
Mira4 | 56 | ||||||
Minia | 675 | ||||||
Newbler | 27 | ||||||
SPAdes | 58 | ||||||
Corynebacterium pseudotuberculosis 1002 (Cp1002) | Ion PGM | Mira3 | 9 | Optical mapping (enzyme kpnI) | 2,335,107 | 5 | [18] |
Mira4 | 12 | ||||||
Minia | 2,425 | ||||||
Newbler | 10 | ||||||
SPAdes | 15 | ||||||
Corynebacterium pseudotuberculosis 12C (Cp12C) | Ion PGM | Mira3 | 25 | Reference (Corynebacterium pseudotuberculosis PAT10) | 2,337,451 | 9 | [22] |
Mira4 | 62 | ||||||
Minia | - | ||||||
Newbler | 17 | ||||||
SPAdes | 631 | ||||||
Corynebacterium pseudotuberculosis VD57 (CpVD57) | Ion PGM | Mira3 | 11 | Reference (Corynebacterium pseudotuberculosis 31) | 2,337,177 | 6 | [23] |
Mira4 | 15 | ||||||
Minia | 1,146 | ||||||
Newbler | 9 | ||||||
SPAdes | 10 | ||||||
Corynebacterium ulcerans FRC11 (FRC11) | Ion PGM | Mira3 | - | Reference (Corynebacterium ulcerans 0102) | 2,442,826 | 6 | [24] |
Mira4 | 30 | ||||||
Minia | 21a | ||||||
Newbler | 9 | ||||||
SPAdes | 8 | ||||||
Corynebacterium ulcerans 210932 (210932) | Ion PGM | Mira3 | 12 | Reference (Corynebacterium ulcerans 0102) | 2,484,335 | 2 | [25] |
Mira4 | - | ||||||
Minia | 343 | ||||||
Newbler | 8 | ||||||
SPAdes | 18 | ||||||
Lactococcus lactis subsp. lactis NCDO 2118 (NCDO2118) | Ion PGM | Mira3 | 661 | Reference (Lactococcus lactis KF147) | 2,554,693 | 18 | [26] |
Mira4 | - | ||||||
Minia | - | ||||||
Newbler | 43 | ||||||
SPAdes | - |