Difference between revisions of "Applications/guppy"

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(Created page with "==Application Details== * Description: ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes. * Version: 1.5.2 (gcc-4.9.3) * Modules: ab...")
 
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===Calculate assembly contiguity statistics===
 
===Calculate assembly contiguity statistics===
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<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
  
 
[username@login] module load abyss/1.5.2/gcc-4.9.3
 
[username@login] module load abyss/1.5.2/gcc-4.9.3
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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.
 
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.
  
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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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.'''
  
 
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.
 
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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#SBATCH -N 2
 
#SBATCH -N 2
 
#SBATCH --ntasks-per-node=40
 
#SBATCH --ntasks-per-node=40
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#SBATCH -o %N.%j.%a.out
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#SBATCH -e %N.%j.%a.err
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#SBATCH --exclusive
 
#SBATCH -t 00:30:00
 
#SBATCH -t 00:30:00
  

Revision as of 15:06, 3 April 2017

Application Details

  • Description: ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
  • Version: 1.5.2 (gcc-4.9.3)
  • Modules: abyss/1.5.2/gcc-4.9.3
  • Licence: Free, open-source

Usage Examples

Assemble a small synthetic data set


[username@login] module load abyss/1.5.2/gcc-4.9.3
[username@login] wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
[username@login] tar xzvf test-data.tar.gz
[username@login} abyss-pe k=25 name=test \
    in='test-data/reads1.fastq test-data/reads2.fastq'

Calculate assembly contiguity statistics


[username@login] module load abyss/1.5.2/gcc-4.9.3
[username@login] abyss-fac test-unitigs.fa

Parallel processing

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.

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.

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.

Note: this example is done on a high memory node, usually access would be achieved with the scheduler


[username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3
[username@c230 ~]$ mpirun abyss-pe np=40

Through SLURM this would become the script:


#!/bin/bash
  
#SBATCH -J abyss
#SBATCH -p highmem
#SBATCH -N 2
#SBATCH --ntasks-per-node=40
#SBATCH -o %N.%j.%a.out
#SBATCH -e %N.%j.%a.err
#SBATCH --exclusive
#SBATCH -t 00:30:00

module purge
module load abyss/1.5.2/gcc-4.9.3

#Run your ABySS commands

abyss-pe name=test k=48 n=8 in='test-1.fa test-3.fa'

Further Information