search

kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
MIT License
9 stars 3 forks source link

add optional flag for writing basecalled fast5s w/ guppy #20

Open kapsakcj opened 4 years ago

kapsakcj commented 4 years ago

This is so someone can run the basecalling script and have it write out basecalled fast5 files, for upload to NCBI/SRA

Something like -u for upload:

run_basecall-w-gpu.sh -i fast5s/ -o outdir/ -k rapid -b y -f r941 -u yes
kapsakcj commented 4 years ago

Need to look into&test if guppy can produce both basecalled fast5s and fastqs at the same time or not

kapsakcj commented 4 years ago

ncbi prefers upload of demultiplexed fastqs, not fast5s. This may be unecessary....