Question: How to trim Nanopore reads. Please suggest a tool.
0
gravatar for Sudosundu
4 months ago by
Sudosundu0
Sudosundu0 wrote:

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.

ont nanopore minionqc • 552 views
ADD COMMENTlink modified 4 months ago by genomax84k • written 4 months ago by Sudosundu0
2
gravatar for genomax
4 months ago by
genomax84k
United States
genomax84k wrote:

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 COMMENTlink modified 4 months ago • written 4 months ago by genomax84k
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