Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-06T17:09:14.293Z
Answers.LastActivityDate: 2021-07-06T17:09:14.293Z
Answers.UserDisplayName: TimD1
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-06T20:44:45.397Z
Answers.LastActivityDate: 2021-07-06T20:44:45.397Z
Answers.UserDisplayName: gringer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-11T19:06:29.207Z
Comments.Text: 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
Comments.UserDisplayName: Maximilian Press
Tags: <r><minion>
Title: How to demultiplex MinION fastQ files without Porechop?
ThreadText: # 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  
  
  ---
  
  ## 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>
  
  
  ---
  
  ### 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>
  
  
  ---
  
  