Basecalling with Guppy(2)¶
We need to specify the following options:
| What? | parameter | Our value |
|---|---|---|
| The config file for our flowcell/kit combination | -c | dna_r9.4.1_450bps_hac_model.cfg |
| Compress the fastq output | –compress_fastq | |
| The full path to the directory where the raw read files are located | -i | ~/workdir/data_artic/barcode_tiny/ |
| The full path to the directory where the basecalled files will be saved | -s | ~/workdir/data_artic/basecall_tiny/ |
| How many worker threads you are using | –cpu_threads_per_caller | 14 |
| Number of parallel basecallers to create | –num_callers | 1 |
Our complete command line using these parameters is:
guppy_basecaller_cpu --compress_fastq -i ~/workdir/data_artic/barcode_tiny/ -s ~/workdir/data_artic/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg