Q2-cutadapt add "--nextseq-trim" option

Ideas and Suggestions
1

Hello !
This option would be really useful for those who deal with data coming from a two-color chemistry platform (NextSeq, NovaSeq, Illumina i100).

The --nextseq-trim will do the same work as the quality cutoff, but will ignore Poly-G tails.

It would take some adaptation for it to work on paired-end data, but two-color chemistry is becoming a standard with Illumina (most of our sequencing partners already switched to i100 and refuse to go back to conventional four-color chemistry)

Here’s the cutadapt documentation: User guide — Cutadapt 5.2 documentation

1 Like
2

Hello Patrick,

Thank you for your suggestion. I've created an issue for it on GitHub:

Is there some special consideration for paired-end data when using -nextseq-trim directly with cutadapt?

3

Well, the –nextseq-trim option is doing the same thing as --p-quality-cutoff-5end, but it will ignore Poly-G tails quality score, so I think you will need two new options (which cannot be used with --p-quality-cutoff):

–nextseq-quality-cutoff-5end
–nextseq-quality-cutoff-3end

Could also be a nextseq “flag” that will switch the -q option to –nextseq-trim under the hood of qiime’s cutadapt.

1 Like
4

That is a great point. Since so many facilities have moved over to NovaSeq and i100 systems, handling those Poly-G tails correctly is essential to avoid losing good data during the filtering step. It would definitely be a valuable addition to the plugin.