Adapters finder

Question

[akis]

Hi,

I am currently studying RNA-seq analysis and have been primarily using the Minion algorithm to find and trim adapters. While this algorithm does not have a large community, it is capable of discovering adapter motifs de novo in addition to finding adapters from a library. I am interested in finding 2-3 similar algorithms to compare and potentially switch to. The data I am working with consists mostly of long reads and is not necessarily paired-end. Can anyone recommend an algorithm that can handle this type of data?

[GenoMax]

Minion algorithm to find and trim adapters

Can you provide a link to what package you are referring to?

You may be best off trying to find this information on Nanopore community site. It is not straight forward to find since ONT does not seem to publish this information in a concise document. I would suggest not using tools that are not meant for long read data.

[akis]

This is the documendation of Minion: https://gensoft.pasteur.fr/docs/reaper/15-065/minion.html

[GenoMax]

it is capable of discovering adapter motifs de novo in addition to finding adapters from a library.

At least one of the adapters looks like this 5’-TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT-3’ rapid adapter. Trying to identify this or something similar in a kilobase long read would be tricky at best. You should also be aware that MinKNOW software has an option to "trim adapters" so you may never see them in the data.

Answer 1

[Axzd]

Would this suit your needs?

https://github.com/OpenGene/fastp

[akis]

This is the one that i ended up with. Although i need to compare more than 2 tools in order gain a better understanding of the pros and cons of each one and eventually, deside which one to keep. If you are aware of any other tool that can handle both given adapters from a library and de novo finding for pair end and single end data, as well as generally long reads, it would be very helpful.

Thank you very much for your responce.

Answer 2

[Juke34]

Some answers here Adapters fro nano pore sequence

https://long-read-tools.org/tools.html?sort=Name&cat=&tec=

[akis]

Thank you very much for your responce.

Is it possible to combine preprocessing with Porechop and Porechop_ABI? Porechop is a tool that detects adapters in libraries, if I recall correctly.