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Table 2 Statistics of Campylobacter jejuni and Chlamydia psittaci contigs compared with results of three assembly tools using MetaQUAST

From: Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics

  Campylobacter jejuni Chlamydia psittaci
assembler IDBA-UD MEGAHIT metaSPAdes IDBA-UD MEGAHIT metaSPAdes
N50 669 681 630 1,057 1,104 974
longest contigs (bp) 1,938 3,004 2,880 4,842 5,732 5,398
genome fraction (%) 2.76 3.84 2.95 52.75 61.90 56.41
misassemblies 0 4 0 11 13 1
mismatches per 100 kb 1,462.90 1,395.01 1,383.12 39.13 45.75 40.68
indels per 100 kb 20.71 18.83 15.40 3.23 3.72 8.62
  1. Campylobacter jejuni 15AD75-1 contigs were compared to reference Campylobacter jejuni ZJB021 (accession no. CP048767.1) and Chlamydia psittaci 15AD75-3 contigs to Chlamydia psittaci GIMC 2005 (accession no. CP024451.1)
  2. The best value for each column is indicated in bold