Difference between revisions of "Applications/ABySS"
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==Application Details== | ==Application Details== | ||
| − | * Description: ABySS is a de novo sequence assembler | + | * Description: ABySS is a de novo sequence assembler. |
* Version: 1.5.2 (gcc-4.9.3) | * Version: 1.5.2 (gcc-4.9.3) | ||
* Modules: abyss/1.5.2/gcc-4.9.3 | * Modules: abyss/1.5.2/gcc-4.9.3 | ||
* Licence: Free, open-source | * Licence: Free, open-source | ||
| + | |||
| + | ==Introduction== | ||
| + | |||
| + | ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes. | ||
==Usage Examples== | ==Usage Examples== | ||
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===Parallel processing=== | ===Parallel processing=== | ||
| − | The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. | + | The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. This will allow you to use multiple cores on a single machine without any MPI configuration. To use multiple machines for assembly, you must create a host file for mpirun, which is described on 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.''' | 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 | + | 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 | '''Note''': this example is done on a high memory node, usually access would be achieved with the scheduler | ||
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| + | |||
| + | [username@login01 ~]$ interactive -phighmem | ||
| + | salloc: Granted job allocation 3619680 | ||
| + | Job ID 3619680 connecting to c231, please wait... | ||
| + | c231.vc-main | ||
[username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3 | [username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3 | ||
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Through '''SLURM''' this would become the script: | Through '''SLURM''' this would become the script: | ||
| − | <pre style=" | + | <pre style="font-family: monospace, sans-serif;"> |
| − | |||
#!/bin/bash | #!/bin/bash | ||
| Line 60: | Line 68: | ||
#SBATCH -o %N.%j.%a.out | #SBATCH -o %N.%j.%a.out | ||
#SBATCH -e %N.%j.%a.err | #SBATCH -e %N.%j.%a.err | ||
| + | #SBATCH -p highmem | ||
#SBATCH --exclusive | #SBATCH --exclusive | ||
#SBATCH -t 00:30:00 | #SBATCH -t 00:30:00 | ||
| Line 69: | Line 78: | ||
abyss-pe name=test k=48 n=8 in='test-1.fa test-3.fa' | abyss-pe name=test k=48 n=8 in='test-1.fa test-3.fa' | ||
| − | |||
</pre> | </pre> | ||
| Line 89: | Line 97: | ||
* qp_srun | * qp_srun | ||
* qp_update | * qp_update | ||
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==Further Information== | ==Further Information== | ||
| − | * [ | + | *[https://www.bcgsc.ca/resources/software/abyss https://www.bcgsc.ca/resources/software/abyss] |
| + | *[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694472/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694472/] | ||
| − | |||
| − | + | {{Modulepagenav}} | |
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Latest revision as of 15:16, 23 August 2023
Contents
Application Details
- Description: ABySS is a de novo sequence assembler.
- Version: 1.5.2 (gcc-4.9.3)
- Modules: abyss/1.5.2/gcc-4.9.3
- Licence: Free, open-source
Introduction
ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
Usage Examples
Assemble a small synthetic data set
[username@login] module add 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 add 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. This will allow you to use multiple cores on a single machine without any MPI configuration. To use multiple machines for assembly, you must create a host file for mpirun, which is described on 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@login01 ~]$ interactive -phighmem salloc: Granted job allocation 3619680 Job ID 3619680 connecting to c231, please wait... c231.vc-main [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 -p highmem #SBATCH --exclusive #SBATCH -t 00:30:00 module purge module add 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'
The Quantum Package has been designed pretty much as an interactive environment for quantum-chemistry calculations, in order to facilitate the user experience.
- qp
- qp_e_conv_fci
- qp_name
- qp_reset
- qp_stop
- qpsh
- qp_convert_output_to_ezfio qp_export_as_tgz
- qp_plugins
- qp_set_frozen_core
- qp_test
- qp_create_ninja
- qp_mpirun
- qp_prepend_export
- qp_srun
- qp_update