Dear all,

I'm new in fungal ITS (internal transcribed spacer) metabarcoding analysis, so please ask if you don't understand my question.

Our lab received Illumina MiSeq sequencing result of our 150 samples from a company, but they give us only the R1 and R2 fastq files, without the consensus sequences. Our lab used to have 454 sequencing previously, and usually we get the consensus sequences. My question is, should we assemble those R1 and R2 into a consensus sequence before further analysis?

We have a pipeline for further analysis which is based on the 454 data, and I'm afraid that if we don't have consensus sequences beforehand, the R1 and R2 sequences would be recognized as two different ITS by the pipeline.

Any idea?

And thanks a lot in advance.
After a few months, I've learnt one or two things about ITS analysis, and one of them is that R1 and R2 reads might be used without merging them beforehand. In fact, we might fail to identify many species using only the merged paired-reads (it's pointed out in [this paper][1], for example).

 [1]: http://dx.doi.org/10.1111/nph.12923