Table 6

GAGE statistics (SNPs, indels and misjoins) on Rhodobacter sphaeroides.

Assembler

SNPs

Indels < 5 bp

Indels ≥ 5 bp

Misjoins

Inv

Reloc


Allpaths-LG

218

150

37

6

0

6

MSR-CA

807

179

32

9

1

8


Allpaths-LG + MSR-CA

GAM-NGS

250

157

44

5

0

5

GAA

345

162

48

5

0

5

ZORRO

263

153

35

7

0

7


MSR-CA + Allpaths-LG

GAM-NGS

842

198

46

10

1

9

GAA

802

187

49

10

1

9

ZORRO

928

215

29

7

0

7



Bambus2

189

149

363

5

0

5

SOAPdenovo

534

155

404

8

0

8


Bambus2 + SOAPdenovo

GAM-NGS

431

173

406

10

0

10

GAA

581

177

404

10

0

10

ZORRO

546

196

84

8

0

8


SOAPdenovo+ Bambus2

GAM-NGS

534

153

393

8

0

8

GAA

532

155

407

8

0

8

ZORRO

513

175

111

9

0

9


For each assembly we show the number of SNPs, the number of indels shorter than 5 bp and greater (or equal) than 5 bp. The number of misjoins is computed as the sum of inversions (parts of contigs reversed with respect to the reference genome) and relocations (rearrangements moving a contig within/between chromosomes).

Vicedomini et al. BMC Bioinformatics 2013 14(Suppl 7):S6   doi:10.1186/1471-2105-14-S7-S6

Open Data