from same lab, same cell line, with good reads ranging from 1.7 to
The question is if that bias is relevant and what you want to achieve with analysing the data, so it seems that your problem is with the semantics of bias rather than the data. What do you want to use the data for?
how to avoid bias:
randomize, e.g. select random samples
stratify, e.g.: make sure your sample is representative of the population structure (e.g. contains as many good and bad sample, and represents the taxon structure, different technology, etc.)
Biases in your data will most certainly manifest in various parameters, such as:
contaminants (you might be able to distinguish labs based on "metagenomics" of contaminants)