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Table 1 Velvet assembly statistics of 108* genomes analyzed at 1605 core meningococcal loci

From: A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

Multiplex group (number of libraries)

Sequence read length

Most common k-mer

Average contig count

Average N50

Average longest contig

Average genome length

Average number of core loci identified

Average number of incomplete loci found

A (12)

54

39

374

18450

66014

2088067

1603

45

B (12)

54

35

407

16252

63032

2073517

1603

39

C (12)

54

39

339

20375

76751

2087187

1602

43

D (12)

54

41

322

22022

79870

2086109

1604

34

E (12)

54

37

396

15813

59228

2108812

1602

43

F (11)

54

41

345

18364

66689

2085872

1603

40

G (12)

54

39

369

16595

61439

2107242

1602

46

H (12)

54

37

329

20557

77125

2095768

1603

46

I (11)

54

39

386

13842

53816

2085635

1604

54

J (7)

54

41

403

22586

104539

2109587

1600

37

K (7)

76

63

295

31378

122718

2143841

1604

26

Average de novo Assembly Statistics

n/a

39

360

19658

75566

2097421

1603

41

  1. *The total number of genomes analysed is 120 and includes: 5 genomes sequenced a second time using 54 base reads (J) and 7 genomes sequenced a second time using 76 base reads (K).
  2. Two genomes failed to sequence in their original groups (F and I), these genomes were subsequently rerun in group J.
  3. The increase in read length used for multiplex group K produced larger than expected assembly improvements. A significant drop in the number of contigs and a corresponding increase in the N50 value were achieved with the relatively small 22 base read increase. Therefore, additional increased base read lengths should continue to increase the coverage of long repeat regions and decrease the number of contigs per assembly.