Decontamination of bacterial isolates is an important step in assuring QC of sequences samples. Multiple tools and algorithms have already been developed to address this issue for second generation sequencing platforms, but for newer systems, such as Oxford Nanopore’s sequencers, there are no viable options. To address these challenges a workflow has been developed which enables cross-contamination detection as well as intra-species contamination of noisy long read sequencing samples. This is done using both k-mer based alignment methods as well as marker gene identification to detect organism present in the sample.
Malte Bjørn Hallgren’s presentation