Nanopore support

[Jonathan Abrahams]

Hi, would you be able to add support for ONT sequencing? I can see an old branch which appears to add a simple flag for KMA.

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Do you know how using pointfinder on ONT-only assemblies differs from assemblies made on other platforms using the current options?

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Kind regards,

Jonathan

[Edison Alain von Matt]

Dear Jonathan,

thank you for your message.

I am unaware of any tests carried out on the difference between ONT-only and other assemblies in Pointfinder. Still, I would assume that a difference will stem from the difference in the results of the alignment tools (Blast and KMA). 

If you submit raw reads while specifying the nanopore flag (-- nanopore), KMA is called inside with the according nanopore specifications. For Blast, however, there does not yet seem to be specific support for ONT sequencing other than using different alignment methods such as NanoBlaster [1].

Apart from that, I have read the following regarding Blast queries using Nanopore reads: "Nanopore queries tend to either match database targets correctly, with very long alignments (hundreds/thousands of identities), or not at all." - [2]

But hopefully, looking through additional and more scientific literature can shine a better light on your question.

Please let me know if you have additional questions.

Best regards

Eddy

[1] M. R. Amin, S. Skiena and M. C. Schatz, "NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads," 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Atlanta, GA, USA, 2016, pp. 1-6, doi: 10.1109/ICCABS.2016.7802776.

[2] http://lonelyjoeparker.com/wp/?p=1417

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