Find an alternative way of handling contamination. For low-level contamination, simply proceed as normal, with higher stringency during shovill assembly, which should exclude contaminating reads from assemblies.
For higher levels of contamination, possibly terminate pipeline and send for re-sequencing or simply fail the sample completely.
dfornika
commented
5 years ago
Find an alternative way of handling contamination. For low-level contamination, simply proceed as normal, with higher stringency during shovill assembly, which should exclude contaminating reads from assemblies.
For higher levels of contamination, possibly terminate pipeline and send for re-sequencing or simply fail the sample completely.