Adapters fro nano pore sequence

Question

[KVC_bioinfo]

Hello All,

I am trying to preprocess the nanopore sequence. I can not find what adaptor sequences are used in it? Are there any adaptor sequence file for this technology?

Thank you very much.

[xum]

I am a scientist at New England Biolabs in Ipswich MA and I noticed that you asked a question concerning Nanopore adaptor for DNA sequencing. I need to design another adaptor that can ligate to DNA fragments first and then anneal to ONT's adaptor. Thanks in advance if you have the feed for the DNA adaptor sequence.

Answer 1

[GenoMax]

https://github.com/rrwick/Porechop#known-adapters

[WouterDeCoster]

That's sufficiently accurate to be an answer in my opinion :-)

[1769mkc]

nanopack doesn't have tool to trim adapter sequence? i used nanofilt to trim though.

[WouterDeCoster]

You can trim a certain number of sequences from the ends, but it doesn't recognize adapters.

[1769mkc]

okay I tried porechop ..but still i do see adapter not sure what isn't it trimming...its nextera adapter in the fastqc reports it says.

[WouterDeCoster]

How does a nextera adapter end up in nanopore sequencing results?

[1769mkc]

not sure i have to ask my collaborator what exactly happened