<p>The Guppy basecaller itself now has the ability to internally perform multiplexing. That is currently the preferred option.</p>
<p>If for some reason, you still want a stand-alone application to demultiplex already basecalled reads, then <code>qcat</code> is an option: <a href="https://github.com/nanoporetech/qcat" rel="nofollow noreferrer">https://github.com/nanoporetech/qcat</a></p>

CC BY-SA 4.0
2021-07-06T17:09:14.293Z
2021-07-06T17:09:14.293Z
TimD1
<p>I have written up my own semi-manual method for demultiplexing Nanopore reads. As distinct from the other methods that are commonly used, it searches the <em>entire</em> read for potential barcode sequences, and splits out identified chimeric reads (containing multiple barcode sequences) into a separate file:</p>
<p><a href="https://dx.doi.org/10.17504/protocols.io.7vmhn46" rel="nofollow noreferrer">https://dx.doi.org/10.17504/protocols.io.7vmhn46</a></p>

CC BY-SA 4.0
2021-07-06T20:44:45.397Z
2021-07-06T20:44:45.397Z
gringer
<p>I recently got fastQ files from a MinION sequencer. I would like to demultiplex these files.</p>
<p>Is there any other software to demultiplex (no porechop) in or outside Artic protocol? I would like to learn options different from porechop.</p>
<p>Thank you!</p>

CC BY-SA 4.0
2021-07-11T19:06:29.207Z
A quick google finds https://bioinformatics.stackexchange.com/questions/7139/demultiplex-nanopore-reads-with-custom-barcodes, https://www.protocols.io/view/demultiplexing-nanopore-reads-with-last-xj3fkqn, https://github.com/nanoporetech/qcat
Maximilian Press
<r><minion>
How to demultiplex MinION fastQ files without Porechop?
# How to demultiplex MinION fastQ files without Porechop?

(Asked by: username_0 on 2021-07-06)

I recently got fastQ files from a MinION sequencer. I would like to demultiplex these files.

Is there any other software to demultiplex (no porechop) in or outside Artic protocol? I would like to learn options different from porechop.

Thank you!

**Tags:** r, minion
> **Comments:**
> **username_1**: A quick google finds https://bioinformatics.stackexchange.com/questions/7139/demultiplex-nanopore-reads-with-custom-barcodes, https://www.protocols.io/view/demultiplexing-nanopore-reads-with-last-xj3fkqn, https://github.com/nanoporetech/qcat  

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## 2 answers

### Answer by username_2 on 2021-07-06. Score: 3 | Accepted answer

The Guppy basecaller itself now has the ability to internally perform multiplexing. That is currently the preferred option.

If for some reason, you still want a stand-alone application to demultiplex already basecalled reads, then `qcat` is an option: <https://github.com/nanoporetech/qcat>


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### Answer by username_3 on 2021-07-06. Score: 1

I have written up my own semi-manual method for demultiplexing Nanopore reads. As distinct from the other methods that are commonly used, it searches the *entire* read for potential barcode sequences, and splits out identified chimeric reads (containing multiple barcode sequences) into a separate file:

<https://dx.doi.org/10.17504/protocols.io.7vmhn46>


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