Fig. 1: Squeegee pipeline workflow.
From: De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee
Squeegee starts with taxonomic classification using Kraken to determine a set of candidate contaminant species. Reads from the input data are aligned to the representative genomes of the candidate contaminant species using Bowtie2 in multi-alignment mode. It also calculates the pairwise Mash distance for all the samples. Then, it combines the prevalence score, the Mash distance, as well as the breadth/depth of genome coverage of the candidates to predict potential contaminants.
