Phase 1: Preprocessing of reads
It is essential to preprocess raw reads before subjecting them for downstream analysis. The preprocessing includes the removal of low quality bases, ambiguous bases and adapter sequences, the stitching together of paired reads, and the detection of chimeric reads. Sequencing errors, reads with ambiguous bases and chimeras can all cause the appearance of spurious OTUs if they are not removed.
Input: raw reads (multiplexed or demultiplexed)
Output: high quality reads ready for OTU picking
Bibliography
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