From dc184ffe36fc6f0b8d0271be3adcab455e7be73e Mon Sep 17 00:00:00 2001 From: Colin Davenport Date: Tue, 26 Mar 2024 10:00:40 +0100 Subject: [PATCH] Update README.md --- README.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 923fe20..714d460 100644 --- a/README.md +++ b/README.md @@ -1,22 +1,25 @@ # guppy_on_slurm -Splitting and accelerating the Oxford Nanopore CPU basecaller guppy using SLURM. + +## March 2024 - only use the Guppy basecaller if you really need to. Guppy has been replaced by the Dorado basecaller by Oxford Nanopore. + +## Splitting and accelerating the Oxford Nanopore CPU basecaller guppy using SLURM. These scripts move FAST5s into subdirectories, then run CPU guppy on each subdirectory independently using a SLURM cluster. -Performance note on GPU vs CPU: important! +## Performance note on GPU vs CPU: important! Guppy is really slow on CPU, but incredibly quick on GPU (100-1000X faster on GPU!). After torturing our 1000+ core cluster for multiple days with CPU basecalling for MinION runs, we finally moved to a performant Nvidia GPU graphics card for basecalling. We use the script `runbatch_gpu_guppy.sh` for this. When using the GPU version, you want to have all your FAST5 files in a single directory, i.e. you do not need to run `bash batch_split_to_subdirs.sh` to split the FAST5 files into subdirectories. Dr. Colin Davenport, June 2019 - August 2021 -Warning: only tested on Ubuntu 16.04 and 20.04 to date (not Windows). Guppy works fine on Ubuntu 20.04, use a singularity container or the native version from ONT. +## Warning: only tested on Ubuntu 16.04 and 20.04 to date (not Windows). Guppy works fine on Ubuntu 20.04, use a singularity container or the native version from ONT. -Requirements +## Requirements * either a working guppy CPU guppy_basecaller (the command `guppy_basecaller` should provide output) * or a singularity guppy CPU container with guppy_basecaller installed in it. * or a Nvidia GPU with CUDA installed -Howto - CPU version: +## Howto - CPU version: 1. Clone the repository