About guppy model

[HW-Superior]

When I go through the first step (the command as guppy_basecaller -i fast5_pass/ -c ~/biosoft/ont-guppy-cpu/data/dna_r10.4.1_e8.2_400bps_sup.cfg --num_callers 10 --cpu_threads_per_caller 5 --save_path fastq --bam_out --moves_out basecall.bam) to get the basecaller.bam file, I wonder how to select guppy's model. Whether to use the -c parameter to select the model. Thnaks!

[umahsn]

Hi, yes -c is how you specify the model.

[HW-Superior]

Hi, the guppy_basecaller is a slow process, is there any way to speed it up. Thanks

[umahsn]

Yes, you can use --device "cuda:0,1" to specify Guppy to use two GPUs if you have more than one available, similarly use --device "cuda:0,1,2" or --device "cuda:0,1,2,4" if you want to use 3 or 4 GPUs. You can also try increasing --gpu_runners_per_device depending upon the memory of your GPU. You can also try to increase --num_callers parameter, and optionally --num_alignment_threads parameter if you are using alignment from Guppy.