Question: Remove adaptaters from ONT reads : An alternative to Porechop ?
1
gravatar for Roxane Boyer
7 months ago by
Roxane Boyer950
France / Toulouse / GeT-Plage
Roxane Boyer950 wrote:

Hello everyone,

I was using Porechop (as everyone I guess) in order to remove adaptaters from ONT reads. This tools is now unsuported (A: Removing adapters from Oxford nano pore reads , 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

ADD COMMENTlink modified 7 months ago by WouterDeCoster39k • written 7 months ago by Roxane Boyer950
3
gravatar for WouterDeCoster
7 months ago by
Belgium
WouterDeCoster39k wrote:

Porechop may be no longer maintained, but it still works.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.

ADD COMMENTlink written 7 months ago by WouterDeCoster39k

"Near future" ;) Alright, I see,

Thanks for the insight then. I'll keep play with Deepbiner tho, because it claims the result contain less than the 30% unclassified reads... Did you ever tried that tool ?

ADD REPLYlink written 7 months ago by Roxane Boyer950

To be honest I don't use barcodes all that often - just one genome per PromethION flow cell ;-)

ADD REPLYlink written 7 months ago by WouterDeCoster39k

I see ;) Bacterial genome with 15000X for the win o/

ADD REPLYlink written 7 months ago by Roxane Boyer950

When do we get these damn flongles :o

ADD REPLYlink written 7 months ago by WouterDeCoster39k

The hype is real o_o

ADD REPLYlink written 7 months ago by Roxane Boyer950
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