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Table 1 Comparative assembly statistics of preliminary assemblies generated using CLC-GWB, Velvet and SOAPdenovo

From: Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research

Assembler

Sex

Optimal kmer (bp)

# contigs

N50 (bp)

% readsa

CLC-GWB

Female

60

251,115

3684

96.0

Male

60

306,273

2487

93.5

Velvet

Female

75

317,916

1095

47.0

Male

75

310,045

956

37.9

SOAPdenovo

Female

75

1,953,762

451

68.8

Male

75

2,010,365

351

58.6

  1. For each assembly pipeline, different kmers were used to generate the optimal assembly, and the main metric for determining quality of assembly was the combination of the number of contigs and the N50
  2. a% reads = the number of reads that mapped to each assembled genome
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BMC Genomics

ISSN: 1471-2164

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