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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
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Question: read group assignment in align_trim #101

Open gianfilippo opened 2 years ago

gianfilippo commented 2 years ago

Hi,

I am just learning how to process Nanopore sequencing data. I am starting from a FASTQ file and trying to understand the artic pipeline.

Could you please explain me how align_trim assigns the read groups ?

Thanks

kakuk9 commented 1 year ago

Hi, I am not a developer, but I also had the same question. According to the artc docs here, during alignment post-processing, it would do "using the derived amplicon, assign each read a read group based on the primer pool".