Comparison of three commercial tools for metagenomic shotgun sequencing analysis

Matthew Thoendel, Patricio Jeraldo, Kerryl E. Greenwood-Quaintance, Janet Yao, Nicholas Chia, Arlen D. Hanssen, Matthew P. Abdel, Robin Patel

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Metagenomic shotgun sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large and complicated data sets is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic shotgun sequencing tools, CosmosID, One Codex, and IDbyDNA, were compared to determine whether they result in similar interpretations of the same sequencing data. We selected 24 diverse samples from a previously characterized data set derived from DNA extracted from biofilms dislodged from the surfaces of resected arthroplasties (sonicate fluid). Sequencing data sets were analyzed using the three commercial tools and compared to culture results and prior metagenomic analysis interpretation. Identical interpretations from all three tools occurred for 6 samples. The total number of species identified included 28 by CosmosID, 59 by One Codex, and 41 by IDbyDNA. All of the tools performed similarly in detecting those microorganisms identified by culture, including polymicrobial mixes. These data show that while all of the tools performed well overall, there were some differences, particularly in their predilection for identifying low-abundance or contaminant organisms as present.

Original languageEnglish (US)
Article numbere00981-19
JournalJournal of clinical microbiology
Issue number3
StatePublished - 2020


  • Diagnosis
  • metagenomics

ASJC Scopus subject areas

  • Microbiology (medical)


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