A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Screenshot 2026-05-28 at 10.26.22.heic

Hello! We are interested in processing sequences from the <https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.13023|515FY/926R> PCR primer pair for both 18S and 16S amplicons. This requires a splitting step during the pipeline (if not, the 18S reads are lost as they do not overlap). Is this possible to do in ampliseq? <https://github.com/jcmcnch/eASV-pipeline-for-515Y-926R|Here> is a pipeline describing it, and <https://www.nature.com/articles/s41597-025-05423-9|here> is the paper. Thank you!

Afaik this is the intended application for <https://nf-co.re/ampliseq/2.17.0/parameters/#mergepairs_strategy|--mergepairs_strategy consensus>. A discussion about that addition is in <https://github.com/nf-core/ampliseq/pull/803>. Let me know if that serves your purpose.

Because I had a minute, I think indeed that approach should aid your approach:
&gt; This approach is particularly beneficial for datasets containing both prokaryotic and eukaryotic sequences, where lengths vary, leading to differing overlap extents.

Hi `--mergepairs_strategy consensus` has been indeed implemented to deal with this primer pair, we've detailed the approach in the supplementary of this preprint: <https://doi.org/10.1101/2025.08.11.669668> , the paper is currently under review

Thank you so much both, that's great! I will try it out :pray: