Hello everyone,

I was using Porechop (as everyone I guess) in order to remove adaptaters from ONT reads. This tools is now unsuported (https://www.biostars.org/p/282767/#282775 , https://github.com/rrwick/Porechop), and with rapid changes in ONT softwares, I'm really afraid it will soon be impossible to use this tools anymore, and I'm looking for alternativ tools.

I found the new tools of Ryan Wick Deepbiner ( https://github.com/rrwick/Deepbinner ), which is presented by him as the sucessor of Porechop, but it is unclear if the tools only demultiplexes reads or also removes the adaptaters from them. For example, I feel like it's impossible to use on non barcoded runs.

Does anyone knows more about that subject ? I've been looking for some ideas on Nanopore Community, but so far my question remains.

Cheers,

Rox


Porechop may be no longer maintained, but it still works. I don't think there is any reason to quickly start looking for alternatives. Based on what I read on the nanopore community forum the adapter removal step would be added to Guppy, the basecaller which is to replace albacore in the "near future". So they (finally) start supporting this themselves.