maximum mismatch by default at merge step between reverse and forward sequences

[arthurs (szylit)]

Hello everyone,

I am currently using QIIME 2 (version: 2023.7) to analyze an amplified gene with primers targeting the V4-V5 region of the small subunit of 16s rRNA in prokaryotes.

I'm at the dada2 step and have a question regarding the merging process. I understand that we provide a parameter for the minimum overlap between the forward and reverse sequences, but is there an option to specify a mismatch error percentage in this overlap region?
Despite my research, I often hear about a 10% allowed error, but I can't find this information. Do you know the default value if we can't specify this information?

Thank you a lot.

[colinvwood (Colin Wood)]

Hello @arthurs,

I understand that we provide a parameter for the minimum overlap between the forward and reverse sequences

You can do this by setting the --p-min-overlap parameter, but people generally only change this if there is a strong reason to do so, most commonly it's left at the default which is 12.

is there an option to specify a mismatch error percentage in this overlap region

There is no parameter exposed by qiime to set the mismatch percentage in the overlap region. From reading dada2's code it looks the max mismatch defaults to 0 (the number of allowed mismatches). If you were using the R tool itself you would be able to change this.