Applications/ABySS - Revision history

Pysdlb at 15:16, 23 August 2023

2023-08-23T15:16:55Z

2023-03-01T16:26:13Z

2023-03-01T16:23:34Z

2022-11-17T14:17:05Z

‎Parallel processing

2022-11-16T16:24:06Z

‎Parallel processing

2022-11-16T16:23:20Z

‎Parallel processing

2022-11-16T16:21:40Z

‎Application Details

2022-11-16T16:21:15Z

2022-11-16T16:20:14Z

2022-11-16T11:19:28Z

@@ Line 99: / Line 99: @@
 ==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/]

@@ Line 99: / Line 99: @@
 ==Further Information==
-*[http://computing.bio.cam.ac.uk/local/doc/abyss.html http://computing.bio.cam.ac.uk/local/doc/abyss.html]
+*[https://www.bcgsc.ca/resources/software/abyss https://www.bcgsc.ca/resources/software/abyss]
 {{Modulepagenav}}

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 ===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 on the mpirun man page.
+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.'''

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 Through '''SLURM''' this would become the script:
-<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
+<pre style="font-family: monospace, sans-serif;">
 #!/bin/bash
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 abyss-pe name=test k=48 n=8 in='test-1.fa test-3.fa'
 </pre>

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 #SBATCH -o %N.%j.%a.out
 #SBATCH -e %N.%j.%a.err
 #SBATCH --exclusive
 #SBATCH -t 00:30:00

@@ Line 46: / Line 46: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3
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 * qp_srun
 * qp_update
 ==Further Information==

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 ==Application Details==
-* Description: ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
+* 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

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 * Modules: abyss/1.5.2/gcc-4.9.3
 * Licence: Free, open-source
 ==Usage Examples==

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