We are trying to analyze Loop Genomics data within QIIME2 (v. 20.20.2) which is full length 16S sequences. The resultant data are assembled contigs of high accuracy. We also noted that the quality scores from the demux summary were very high across reads (> 30 phred score), and so we only trimmed down to 1500 nucleotides to ensure that most reads were of a similar length. We tried running dada2 denoise-single with the command below, but it ended up filtering all but 5% of our reads, which is much too low. Do we need to adjust the value of --p-max-ee to a higher value? We don’t have the ability to do experimental testing on a mock community, but we were hoping that someone may have encountered long read data before and have a rough recommendation on what to set this value at. Or if there are additional things we should try instead?
qiime dada2 denoise-single \ --i-demultiplexed-seqs single-end-demux.qza \ --p-trim-left 0 \ --p-trunc-len 1500 \ --o-representative-sequences rep-seqs-dada2.qza \ --o-table table-dada2.qza \ --o-denoising-stats stats-dada2.qza