- No file added yet -
The effect of contaminated reference genomes in clinical metagenomics (Item B)
This item is shared privately
figure
modified on 2018-05-21, 11:15 The importance of using curated microbial reference genome databases.
Classifying unfiltered quality trimmed reads using a Kraken database composed of non-curated microbial reference genomes and the human reference results in the identification of many reads that are mapping to Toxoplasma gondii and Plasmodium vivax. In fact, these genomes recruit more reads than the causing agent Enterococcus faecalis. The classification is improved when human DNA sequences are filtered out prior to classification and a cleaned reference database is used.
The sankey diagrams were created using Pavian (https://www.biorxiv.org/content/early/2016/10/31/084715).
Classifying unfiltered quality trimmed reads using a Kraken database composed of non-curated microbial reference genomes and the human reference results in the identification of many reads that are mapping to Toxoplasma gondii and Plasmodium vivax. In fact, these genomes recruit more reads than the causing agent Enterococcus faecalis. The classification is improved when human DNA sequences are filtered out prior to classification and a cleaned reference database is used.
The sankey diagrams were created using Pavian (https://www.biorxiv.org/content/early/2016/10/31/084715).
Reference
Kirstahler P, Bjerrum SS, Friis-Møller A, la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid. Scientific Reports, doi:10.1038/s41598-018-22416-4.
