New subworkflow and module to assess polyG error in NovaSeq X Plus data

[MatthiasZepper]

Description of feature

A new error mode has been observed in Illumina NovaSeq X data. Some reads exhibit artificial interspersed poly-G sequences. Now, Brian Bushnell has released a new tool, that can (in combination with other tools from the BBTools suite) filter the affected reads.

We would like to quantify the number of affected reads by default for new projects. Therefore, we should include an assessment into Seqinspector.

This entails:

• A new module for BBTools PolyFilter
• A new subworkflow, that combines it with BBDuk as described on Biostars.
• A new MultiQC module / custom content config that plots this information

[FranBonath]

Is this now possible in Multiqc / Fastqc / Fastqscreen? I have seen Adapter graphs that contain also poly-G per sample...

[FranBonath]

Task: check out Multiqc and it's feature of showing poly-G. Figure out what we have to do to add this to seqinspector. If it is native to a newer version of Multiqc, this issue can be solved with an explanation on how to get it in (for example, what version of Multiqc is needed, what settings need to be set, etc.)

[MatthiasZepper]

No, this can certainly not be done solely with MultiQC. I still think it is a very useful addition to the pipeline, but doesn't have to be in version 1.0, if there is no capacity for it.

[FranBonath]

ok, in that case, it would be really nice to have this specific tool included. BUT this will not be included in V1.