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hoelzer / mgnify-lr

Evaluation of long-read support for the MGnify pipeline
GNU General Public License v3.0
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Add basecalling support #4

Open hoelzer opened 4 years ago

hoelzer commented 4 years ago

If a folder with FAST5 files is provided perform basecalling with guppy and then start the assembly pipleine.

see https://github.com/replikation/docker_pipelines/blob/master/modules/basecalling.nf

hoelzer commented 4 years ago

Actually this would be a really good feature because the pipeline has then full control over the model used for basecalling that can then be subsequently used for polishing in medaka