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2.8 years ago
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I need to find a tool to trim the barcodes from my Nanopore long reads. I'm looking for an alternative to Porechop since that program is no longer maintained. Can someone recommend a tool that they have used for trimming barcodes from nanopore reads?
Thank you for the help!!
Are the reads demultiplexed already or do you want a software that does both demultiplexing and adaptor removal?
My reads are demultiplexed already.
Guppy should have removed the adaptors as it does the demultiplexing. If you think you still have some adaptors left then you can use Porechop or qcat. They are both no longer maintained but they should work, unless your library kit is newer and not included in either of them. I'm not aware of any other software for just adaptor removal specifically for Nanopore.
maybe give it a go with guppy_barcoder, which does demultiplexing (re-demultiplexing in your case), and it can also trim off barcodes.