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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 -
  1. aMinia assembled only 8,097 bp of the genome
  2. -The assembly fails for an unknown reason