Trimming nanopore reads

Question

[Nodilan]

Good morning ,

Can I use trimmomatic in order to trim my reads generated using nanopore technology ?

thanks,

Answer 1

[colindaven]

Yes, but it probably will not work well, as nanopore read trimming was not Trimmomatics' intended data type.

Have a look at Fastp, chopper or the Porechop_ABI fork of Porechop https://github.com/bonsai-team/Porechop_ABI

Seqtk is another possibility.

Answer 2

[cfos4698]

I recommend using nanoq or filtlong for quality/length filtering/trimming of nanopore reads

[Nodilan]

can I still use fastqc and multiqc to check the quality of my nanopore reads ?

[GenoMax]

While you can, you will want to use a package meant for long reads like PycoQC. It requires the sequencing_summary file from the nanopore run.

[colindaven]

You can, but I'd use Fastp and Multiqc instead. Faster and better output of %Q20 and %Q30 reads for ONT (in my opinion). Also PycoQC and or the Nanoplot / Nanopack toolset https://github.com/wdecoster/nanopack might be useful.

[zau saa]

This page may help https://help.nanoporetech.com/en/articles/6628901-should-i-qc-my-data-and-what-tools-to-use