Known reagent- and laboratory-contaminant genera — known_contaminant

A curated vector of bacterial genera repeatedly reported as reagent, kit and laboratory contaminants in low-biomass sequencing studies. The list is compiled from Salter et al. (2014), the micRoclean workflow and the GRIMER contaminants.yml / human-related.yml resources. It is intended as a starting blocklist for contam_blocklist_pq(); users should adapt it to their own substrate and primers.

Usage

known_contaminant_genera()

Value

A character vector of genus names.

References

Salter SJ, Cox MJ, Turek EM, et al. (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biology 12:87. doi:10.1186/s12915-014-0087-z

Author

Adrien Taudière

Examples

head(known_contaminant_genera())
#> [1] "Afipia"        "Aquabacterium" "Asticcacaulis" "Aurantimonas" 
#> [5] "Beijerinckia"  "Bosea"        
length(known_contaminant_genera())
#> [1] 83