Difference between revisions of "ABySS"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:De Novo]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|abyss}} | |{{#vardefine:app|abyss}} | ||
Latest revision as of 16:17, 19 August 2022
Description
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.
Environment Modules
Run module spider abyss to find out what environment modules are available for this application.
System Variables
- HPC_ABYSS_DIR - installation directory
How To Run
The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default:
export HPC_USE_MPIEXEC=1