nanoporetech
Dorado read error correction: calling model for R9.4.1
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:
- Dorado version: dorado-0.7.1-linux-x64
- Dorado command:
dorado correct - Source data type (e.g., pod5 or fast5 - please note we always recommend converting to pod5 for optimal basecalling performance): fastq
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
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
At this time dorado correct only has support for the R10.4.1 herro model.
Kind regards, Rich
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