Entering edit mode
6 months ago
Maxwell
▴
70
Im trying to have some different educated views on the minimal quality control thresholds that must be applied in shotgun or amplicon metagenomics for non assembly based analysis. Generally this would likely apply most to kmer based analysis.
This is besides removing adapter sequences. For example, what would be the minimal parameters to tweak and their thresholds in fastp?
Can we not do any analysis what so ever without some quality control threshold ? as in we need to trim minimally reads that are below an average phred score of 25, or each BP must be at the very least 20 or 25, or trimming xyz tail, or complexity threshold, or a minimal read length etc.
Can anyone elaborate on this, potentially looking for discussion.
