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Install

CPU Version

https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu-5.0.11-win64.msi

wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.0.1_linux64.tar.gz
tar -zvxf ont-guppy-cpu_6.0.1_linux64.tar.gz
cd ont-guppy-cpu
bin/guppy_basecaller --version
# or
/scratch/work/chengg1/ont-guppy-cpu/bin/guppy_basecaller --version

Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 6.0.1+652ffd1

GPU Version

wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_6.0.1_linux64.tar.gz
tar -zvxf ont-guppy_6.0.1_linux64.tar.gz

module load gcc
module load cuda
cd ont-guppy-cpu
bin/guppy_basecaller --version

Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 6.0.1+652ffd1

Usage

Demo 1: Taiyaki Walk-through

cd /scratch/cs/nanopore/chengg1/base_calling/dataset/taiyaki_walkthrough

/scratch/work/chengg1/ont-guppy-cpu/bin/guppy_basecaller -i reads -s basecalls -c /scratch/work/chengg1/ont-guppy-cpu/data/dna_r9.4.1_450bps_hac.cfg

module load gcc
module load cuda
/scratch/work/chengg1/ont-guppy/bin/guppy_basecaller -i reads -s basecalls -c /scratch/work/chengg1/ont-guppy/data/dna_r9.4.1_450bps_hac.cfg --device cuda:0

image

--fast5_out                           Choice of whether to do fast5 output.
-r [ --recursive ]                    Search for input files recursively.
--disable_pings                       Disable the transmission of telemetry pings.

Config

guppy_basecaller --print_workflows
flowcell kit barcoding config_name model version
FLO-FLG001 SQK-RNA001 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b
FLO-FLG001 SQK-RNA002 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b
FLO-MIN106 SQK-RNA001 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b
FLO-MIN106 SQK-RNA002 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b
FLO-MINSP6 SQK-RNA001 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b
FLO-MINSP6 SQK-RNA002 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b
FLO-MIN107 SQK-RNA001 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b
FLO-MIN107 SQK-RNA002 rna_r9.4.1_70bps_hac 2020-09-07_rna_r9.4.1_minion_256_8f8fc47b

Reference

  1. https://timkahlke.github.io/LongRead_tutorials/BS_G.html
  2. https://denbi-nanopore-training-course.readthedocs.io/en/latest/basecalling/basecalling_1.html