ABySS - Revision history

Samuel Lampa (UPPMAX) at 13:57, 29 September 2011

2011-09-29T13:57:39Z

Samuel Lampa (UPPMAX) at 13:55, 29 September 2011

2011-09-29T13:55:43Z

Samuel Lampa (UPPMAX) at 13:53, 29 September 2011

2011-09-29T13:53:47Z

Samuel Lampa (UPPMAX) at 13:53, 29 September 2011

2011-09-29T13:53:34Z

Samuel Lampa (UPPMAX): Created page with "{{software info |description=A parallel assembler for short read sequence data |license=Other |fields=bioinformatics }} ABySS is a de novo, parallel, paired-end sequence assemb..."

2011-09-29T13:52:19Z

Created page with "{{software info |description=A parallel assembler for short read sequence data |license=Other |fields=bioinformatics }} ABySS is a de novo, parallel, paired-end sequence assemb..."

New page

{{software info
|description=A parallel assembler for short read sequence data
|license=Other
|fields=bioinformatics
}}

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

If you need larger kmer size please load the module abyss/1.2.7-maxk96.

To run AbySS on Kalkyl use the module system. NB! The later versions of ABySS only work with the gcc compiler. To be on the safe side. Remember to specify the versions used, not the default.

module load gcc openmpi
module load bioinfo-tools abyss

=== Run in parallel in slurm ===

#!/bin/bash -l
#SBATCH -J abysstest
#SBATCH -o abysstest.output
#SBATCH -e abysstest.error
#SBATCH --mail-user smurf@smurfland.se
#SBATCH --mail-type=ALL
#SBATCH -t 02:00:00
#SBATCH -A b2010999 #Use one node with 8 cores
#SBATCH -p node -n 8
module load gcc openmpi
module load bioinfo-tools abyss/VERSION
abyss-pe np=$SLURM_NPROCS ...(your options)

== Publisher ==
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
* '''Website:''' http://www.bcgsc.ca/platform/bioinfo/software/abyss

@@ Line 2: / Line 2: @@
 {{software info
 |description=A parallel assembler for short read sequence data
-|license=other
+|license=free
 |fields=bioinformatics
 }}
 == Availability ==
 {{list resources for software}}

@@ Line 20: / Line 20: @@
 To run AbySS on Kalkyl use the module system. NB! The later versions of ABySS only work with the gcc compiler. To be on the safe side. Remember to specify the versions used, not the default.
-    module load gcc openmpi
+ module load gcc openmpi
-    module load bioinfo-tools abyss
+ module load bioinfo-tools abyss
 === Run in parallel in slurm ===

@@ Line 4: / Line 4: @@
 |fields=bioinformatics
 }}
 ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.