Nanopore

skip / pass / fail data

There are 3 categories to be found in various nanopore runs:

• pass: reads have an average quality score > Q7
• fail: reads have an average quality score < Q7
• skip: reads that were not basecalled due to time constraints

Basecalling nanopore

Check out the workflows available:

guppy_basecaller --print_workflows

then,

guppy_basecaller --compress_fastq -i fast5_pass/barcode01/ -s myfastq --cpu_threads_per_caller 2 --num_callers 4 -c dna_r10.4.1_e8.2_400bps_hac.cfg

when you add .cfg at the end of the chosen workflow