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Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Dorado read error correction: calling model for R9.4.1 #921

Open changsarahl opened 3 months ago

changsarahl commented 3 months ago

Issue Report

Dorado read error correction: calling model for R9.4.1

Please describe the issue:

Hi, I would like to use the dorado correct function to correct R9.4.1 data, but it is unclear where to retrieve this model for use within dorado correct.
The github mentions running model weights with this code: 

$ dorado download --model herro-v1
$ dorado correct -m herro-v1 reads.fastq(.gz) > corrected_reads.fasta

However, there is no documentation on the type of model that would be used for R9.4.1 data.

The original HERRO documentation mentions the experimental model for R9.4.1 (https://github.com/lbcb-sci/herro?tab=readme-ov-file#model-download), but I cannot find whether it is currently implemented into the current version of dorado correct.

Run environment:

HalfPhoton commented 3 months ago

The model used by dorado correct is the same as the one use by HERRO for r10.4 data.

As such dorado correct is not supported for r9.4.1 data unfortunately.

We're looking at adding support for r9.4.1 in the future.

Kind regards, Rich

asan-emirsaleh commented 2 weeks ago

Hello @HalfPhoton ! Could you please clarify, are there any progress in adding the model for r9.4.1? Herro has an experimental model for r9.4.1, is it suitable for adding?

Best regards Asan

HalfPhoton commented 2 weeks ago

At this time dorado correct only has support for the R10.4.1 herro model.

Kind regards, Rich

HalfPhoton commented 1 week ago

Hi @changsarahl, At this time we're not planning on adding support for the R9.4.1 condition / models in dorado correct

Kind regards, Rich