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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.