Question: Adapters fro nano pore sequence
0
gravatar for KVC_bioinfo
3.0 years ago by
KVC_bioinfo510
Boston
KVC_bioinfo510 wrote:

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.

nanopore adaptor • 3.6k views
ADD COMMENTlink written 3.0 years ago by KVC_bioinfo510

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.

ADD REPLYlink written 4 months ago by xum0
4
gravatar for genomax
3.0 years ago by
genomax92k
United States
genomax92k wrote:

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

ADD COMMENTlink written 3.0 years ago by genomax92k
2

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

ADD REPLYlink written 3.0 years ago by WouterDeCoster44k

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

ADD REPLYlink written 5 weeks ago by krushnach80850

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

ADD REPLYlink written 5 weeks ago by WouterDeCoster44k

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.

ADD REPLYlink written 5 weeks ago by krushnach80850

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

ADD REPLYlink written 5 weeks ago by WouterDeCoster44k

not sure i have to ask my collaborator what exactly happened

ADD REPLYlink written 5 weeks ago by krushnach80850
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