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Difference between revisions of "Applications/guppy"

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==Application Details==
 
==Application Details==
  
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* Description: ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
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* Description: Local accelerated basecalling for Nanopore data.
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* Version: 1.5.2 (gcc-4.9.3)
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* Version: guppy 3.1.5
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* Modules: abyss/1.5.2/gcc-4.9.3
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* Modules: guppy/cpu/3.1.5 and guppy/gpu/3.1.5 (GPU)
 
* Licence: Free, open-source
 
* Licence: Free, open-source
  
 
==Usage Examples==
 
==Usage Examples==
  
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===Assemble a small synthetic data set===
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===Batch example===
  
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
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This uses 2 GPUs presently on GPU05 (compute level is high than 6) which is required by guppy's minimum requirement.
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[username@login] module add abyss/1.5.2/gcc-4.9.3
 
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[username@login] wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
 
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[username@login] tar xzvf test-data.tar.gz
 
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[username@login} abyss-pe k=25 name=test \
 
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    in='test-data/reads1.fastq test-data/reads2.fastq'
 
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</pre>
 
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===Calculate assembly contiguity statistics===
 
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
 
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[username@login] module add abyss/1.5.2/gcc-4.9.3
 
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[username@login] abyss-fac test-unitigs.fa
 
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</pre>
 
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===Parallel processing===
 
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The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single machine. To use multiple machines for assembly, you must create a hostfile for mpirun, which is described in the mpirun man page.
 
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Do not run '''mpirun -np 8 abyss-pe'''. To run ABySS with 8 threads, use '''abyss-pe np=8'''. The abyss-pe driver script will start the MPI process, like so: '''mpirun -np 8 ABYSS-P.'''
 
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The paired-end assembly stage is multithreaded, but must run on a single machine. The number of threads to use may be specified with the parameter j. The default value for j is the value of np.
 
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'''Note''': this example is done on a high memory node, usually access would be achieved with the scheduler
 
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
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[username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3
 
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[username@c230 ~]$ mpirun abyss-pe np=40
 
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</pre>
 
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Through '''SLURM''' this would become the script:
 
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
  
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<pre>
 
#!/bin/bash
 
#!/bin/bash
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#SBATCH -J guppy.job
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#SBATCH -J abyss
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#SBATCH --exclusive
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#SBATCH -p highmem
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#SBATCH -o gpu05.%j.out
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#SBATCH -N 2
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#SBATCH -e gpu05.%j.err
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#SBATCH --ntasks-per-node=40
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#SBATCH -p gpu05
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#SBATCH -o %N.%j.%a.out
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#SBATCH --gres=gpu:tesla:2
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#SBATCH -e %N.%j.%a.err
 
 
#SBATCH --exclusive
 
#SBATCH --exclusive
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#SBATCH -t 00:30:00
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module purge
 
module purge
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module add abyss/1.5.2/gcc-4.9.3
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module load cuda/10.1.168
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module load guppy/gpu/3.1.5
  
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#Run your ABySS commands
 
  
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abyss-pe name=test k=48 n=8 in='test-1.fa test-3.fa'
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guppy_basecaller --input_path /home/user/fast5 --save_path /home/user/guppy --flowcell FLO-MIN106 --kit SQK-RPB004 --min_qscore 7 --qscore_filtering -x cuda:0 cuda:1
  
 
</pre>
 
</pre>
  
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The Quantum Package has been designed pretty much as an interactive environment for quantum-chemistry calculations, in order to facilitate the user experience.
 
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* qp                         
 
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* qp_e_conv_fci             
 
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* qp_name                   
 
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* qp_reset                   
 
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* qp_stop                   
 
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* qpsh
 
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* qp_convert_output_to_ezfio  qp_export_as_tgz           
 
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* qp_plugins                 
 
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* qp_set_frozen_core         
 
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* qp_test
 
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* qp_create_ninja           
 
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* qp_mpirun                 
 
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* qp_prepend_export         
 
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* qp_srun                   
 
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* qp_update
 
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* |>
 
  
  
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==Further Information==
 
==Further Information==
  
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* [http://computing.bio.cam.ac.uk/local/doc/abyss.html http://computing.bio.cam.ac.uk/local/doc/abyss.html]
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* https://community.nanoporetech.com/ (login required)
  
 
==Navigation==
 
==Navigation==

Revision as of 13:59, 14 June 2019

Application Details

  • Description: Local accelerated basecalling for Nanopore data.
  • Version: guppy 3.1.5
  • Modules: guppy/cpu/3.1.5 and guppy/gpu/3.1.5 (GPU)
  • Licence: Free, open-source

Usage Examples

Batch example

This uses 2 GPUs presently on GPU05 (compute level is high than 6) which is required by guppy's minimum requirement. 

#!/bin/bash
#SBATCH -J guppy.job
#SBATCH --exclusive
#SBATCH -o gpu05.%j.out
#SBATCH -e gpu05.%j.err
#SBATCH -p gpu05
#SBATCH --gres=gpu:tesla:2
#SBATCH --exclusive


module purge
module load cuda/10.1.168
module load guppy/gpu/3.1.5


guppy_basecaller --input_path /home/user/fast5 --save_path /home/user/guppy --flowcell FLO-MIN106 --kit SQK-RPB004 --min_qscore 7 --qscore_filtering -x cuda:0 cuda:1



Further Information

Navigation

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