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https://github.com/rrwick/Porechop is a tool specifically developed and used for removing adapter sequences from nanopore libraries. Unfortunately can be quite slow and is abandoned by the creator for difficulties in keeping it up and running as you can see on the github page. That being said the tool is functional and it does work. It also provides an option to remove reads which detect the presence of a different barcode sequence in the middle of it which seems like a safer bet. As mentioned, this command can take quite a bit of time to complete so consider modifying the following command to work only on one of the the raw sequencing files that only has 4,000 reads in it if you are just looking for an overview of the program and dont plan to run the assembly afterwords.
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porechop -t 48 -i barcode01.combined.trimmed.fastq -o barcode01.combined.adapter-trimmed.fastq.gz --discard_middle |
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