Paired-end sequnces of 16S rRNA are not merged.

Question

[shabegmatov]

Hey there, colleague. I am trying to merge paired-end sequences of 16S rRNA by FLASH software. But, I am getting only less than 3% of merged reads. Why I am getting so low a percent of seqs?

Answer 1

[colindaven]

They are probably not overlapping enough (read ends are often low quality and thus trimmed off).

You could try the nice nf-core ampliseq pipeline. I had a similar experience with poorly overlapping data and could only use single ended 16S in one project once.