There are several widely used tool collections, e.g., QIIME 2 [13], mothur [14], usearch [15], and vsearch [16], and 1-stop pipelines, e.g., LotuS [17], with new approaches continually being developed, e.g., OCToPUS [18] and PEMA [19]

If your data is high quality, you want improved taxonomic resolution, and you are not concerned about the intra-genomic heterogeneity in the targeted marker genes, an ESV-based approach could be advantageous. Otherwise, a more standard OTU-based approach might be your best bet.

Chimeric reads occur when one sequencing read aligns to two distinct portions of the genome with little or no overlap. Chimeric reads are indicative of structural variation. Chimeric reads are also called split reads.

Various algorithms are available for this process2

Next generation sequencing data analysis

Improved Protocols for Illumina Sequencing

Modified hybridization buffers.

FAQ on FASTA/Q manipulations