How to trim Nanopore reads. Please suggest a tool.

Question

[SUDOsundu]

Hi all,

I checked the Nanopore basecalled reads using MinION QC tool. From what I've understand, I need to select only the reads which are passed the N50 value. MinION QC gives the information only. Now how to select those passed reads from the data. Which tool to be used to select the best quality reads and to trim? I am not a bioinformatician. But trying to become one.

[WouterDeCoster]

From what I've understand, I need to select only the reads which are passed the N50 value.

Based on what did you get this idea?

Answer 1

[GenoMax]

You may be able to use nanofilt which is part of a suite of tools called nanopack written by @Wouter DeCoster. If you have not used these tools before you may want to get the full suite.

Note: Trimming and filtering are two different operations. Since title of your post says trimming, you may be able to use other trimmers (bbduk.sh from BBMap suite, trimmomatic etc) for that analysis.

Answer 2

[MohammadAlkadi]

I used https://github.com/rrwick/Porechop and I am satisfied.

[pbpanigrahi]

Its good but its no longer supported. So use cautiously.

Answer 3

[Juke34]

The complete list is available here https://long-read-tools.org/tools.html?sort=Name&cat=&tec=
Add filter with "Quality Trimming"

Answer 4

[elizabethmareeross]

We recently made a tool exactly for this: Prowler - https://www.biorxiv.org/content/10.1101/2021.05.09.443332v1.full.pdf It is inspired by short read QC programs to pick the good sections out of reads even when the entire read would fail nanofilt because it has low quality areas. We made it because some of our longest reads were failing QC even though they had large stretches of good data.