ALLPATHS-LG is a short read genome assembler from the Computational Research and Development group at the Broad Institute.

The ALLPATHS-LG home page is at

Available modules

Packages with modules

Module NeSI Cluster
ALLPATHS-LG/50041-goolf-1.5.14 pan
ALLPATHS-LG/46968-goolf-1.5.14 pan

Licensing requirements

ALLPATHS-LG is made available at no cost subject to a permissive open-source licence, the full text of which is available at

Example scripts

Example script for the Pan cluster

#!/bin/bash -e

#SBATCH --job-name      ALLPATHS-LG_job
#SBATCH --account       nesi99999
#SBATCH --time          01:00:00
#SBATCH --mem-per-cpu   4G
#SBATCH --output        ALLPATHS-LG_job.%j.out # Include the job ID in the names
#SBATCH --error         ALLPATHS-LG_job.%j.err # of the output and error files

module load ALLPATHS-LG/50041-goolf-1.5.14

# Arguments are from the basic example in the ALLPATHS-LG documentation; please
# modify them as necessary
srun RunAllPathsLG PRE=/assemblies DATA=datadir RUN=rundir SUBDIR=attempt1


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