How to trim Nanopore reads. Please suggest a tool.
4
4
Entering edit mode
2.9 years ago
SUDOsundu ▴ 60

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.

Nanopore MinIONQC ONT • 8.4k views
ADD COMMENT
1
Entering edit mode

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?

ADD REPLY
5
Entering edit mode
2.9 years ago
GenoMax 122k

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.

ADD COMMENT
2
Entering edit mode
21 months ago

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

ADD COMMENT
1
Entering edit mode

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

ADD REPLY
2
Entering edit mode
17 months ago

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.

ADD COMMENT
1
Entering edit mode
17 months ago
Juke34 7.3k

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

ADD COMMENT

Login before adding your answer.

Traffic: 889 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6