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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
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Primer trimming #20

Closed thierryjanssens closed 2 years ago

thierryjanssens commented 2 years ago

Hello Saskia,

in which step did you include the step for removal of primer sequences? If any.

kind regards,

Thierry

Saskia-Oosterbroek commented 2 years ago

Hi Thierry,

At this moment primer removal is not incorporated. If you use the demultiplex option barcodes+adapters are removed by qcat. However qcat is still working, it has been archived and it's support discontinued. I actually recommend demultiplexing with Guppy. Removal of primer sequences has worked well for me with Cutadapt (https://cutadapt.readthedocs.io/en/stable/guide.html).

Best, Saskia