search

wdecoster / chopper

MIT License
151 stars 12 forks source link

Question: HiFi adapters #43

Closed diegomics closed 1 month ago

diegomics commented 1 month ago

Hi devs, is there a way to discard reads where SMRTbell adapter are detected? Can the --contam flag be used for that? Thx :)

wdecoster commented 1 month ago

Hi,

I don't think that is currently possible, is that a frequent problem?

--contam won't work, as that requires a large overlap between read and contaminant, at least 90% of the read has to align to the contaminant.

Best, Wouter

diegomics commented 1 month ago

Ok, I see. It happens, an artifact of CCS. Adapter detection is part of current VGP assembly recommended workflow: "However, due to the nature of SMRT sequencing technology, adapters do not have a specific, predictable location in HiFi reads. Additionally, the reads containing adapter sequences could be of generally lower quality compared to the rest of the reads. Thus, we will use cutadapt not to trim but to remove the entire read if a read is found to have an adapter inside of it." It may be a nice addition to the tool to make it more universal. Thanks for the reply!