nanopore mode in Resfinder

[Aldert Zomer]

Hi,
Would it be possible to have a Nanopore mode that invokes the -bcNano option in kma? And I'm not sure if Resfinder is using blastn -task blastn or blastn -task megablast (default setting of blastn), but in the latter case, also blastn -task dc-megablastn when using the Nanopore mode.
thanks

Aldert

[Alfred Ferrer Florensa]

Hi Aldert,

‌

I have been talking with several coworkers and, although we want to improve that part of our software, we are waiting for some improvements in KMA in Nanopore data to apply it in our software. Besides that, we are working in a new version of the CGE module, and that should include the options of using the nanopore option in kma (and blastn, as right now is using the default setting).

‌

Alfred

[Aldert Zomer]

I did make the change in the CGE module, but then it sometimes fails the run, also in the test case.

[Alfred Ferrer Florensa]

I see.

However, we think it is better to add this option with the improvement in kma for nanopore data is done. If it is before the new cge module, it will be added also to the old version.

About blast, resfinder do not use blast on nanopore data, as it only uses blast on already assembled data

[RolfKaas]

Nanopore option has been implemented