ILRI Research Computing

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====== guppy ======
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing features.

See this tutorial: https://denbi-nanopore-training-course.readthedocs.io/en/latest/basecalling/basecalling.html

===== Information =====

  * Version: 6.5.7
  * Added: July, 2021
  * Updated: December, 2023

===== Usage =====
Guppy is only available on compute06 because this is the only node that has a GPU.

//Note: guppy ships with some pre-configured models that set many basecalling parameters to sensible defaults. Please consult: /opt/ont/guppy/data.//
===== Installation ======

Notes from the sysadmin during installation.

<code>$ sudo dnf install https://hpc.ilri.cgiar.org/~jbaka/ONT-Dec2023/Software/ont-guppy-6.5.7-1.el8.x86_64.rpm</code>

Run some test data using fourteen CPUs:

<code>$ mkdir -p /var/scratch/aorth/2022-05-24-guppy
$ cd /var/scratch/aorth/2022-05-24-guppy
$ wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group1.tar.gz
$ tar xf Data_Group1.tar.gz
$ guppy_basecaller --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg
...
Caller time: 3281435 ms, Samples called: 27619692, samples/s: 8416.96</code>

Run some test data using a GPU (currently only on compute06):

<code>$ srun --gres=gpu:v100:1 --partition=batch -w compute06 -n 1 -J guppy --pty bash
$ guppy_basecaller --device "cuda:0" --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg
...
Caller time: 4366 ms, Samples called: 27619692, samples/s: 6.32609e+06</code>