I have fastq.qz files that is prepared as described below,
I was able to import it to qiime 2 and denoised it again using dada2 to create featured table, my question is how can I create featured table without going through dada2 since my files are already denoised if I understood it right.
16S amplicons from each sample are individually barcoded and sequenced in multiplex in the NextSeq 500 platform in a 150bp paired-end modality. Raw data from the sequencer is first demultiplexed, and the forward and reverse reads obtained in each of the 4 lanes per sample are filtered using the following criteria:
- both forward and reverse reads in a pair must have an average Q-score > 30
- primers, and any leading random nucleotides (used to increase diversity of the library being sequenced) are trimmed, and forward reads are capped at 125bp and reverse reads are capped at 124bp
- forward and reverse reads of each pair are appended, and those sequences that contain more than 8 consecutive same nucleotide repeats are discarded
- the remaining sequences are clustered using a distance of 1 nucleotide using the Swarm algorithm1, and the most abundant sequence per cluster is considered the representative of the cluster and it is assigned a count corresponding to the sum of sequences that compose the cluster
- a chimera removal using these centroid representative sequences is performed using the VSEARCH uchime_denovo algorithm2. Singletons that remain after chimera removal are also discarded.
- Finally, both forward and reverse reads that match with at least 77% sequence identity to the same sequence in version 123 of the SILVA database3 are assumed to be 16S sequences
Below is how the Fastq file looked like: