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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
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Recommended procedure for profiling nanopore data #480

Closed bcpd closed 2 months ago

bcpd commented 2 months ago

Description of feature

Could you recommend what the current best practices around taxonomic profiling of nanopore data (r10.4.1) are? Many thanks - and thank you for developing this tool.

jfy133 commented 2 months ago

Hi @bcpd

Within taxprofiler there isn't currently any particular guidance other than make sure your database parameters are adapted for long reads.

I would recommend checking the literature for specific advice on which tools would be most suitable for your particular project and compare with what is available in the pipeline.

Note that our next major release (1.2) will extend to more long-read specific profilers, but it isn't really the purpose of the pipeline to describe 'best practises' of specific data types (as it normally depends on the project...0