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AllPaths-LG is a short read genome assembler from the Computational Research and Development group at the Broad Institute. AllPaths-LG v49967 is installed across all HPC nodes.


AllPaths-LG can be loaded as a module

[asrini@node062 ~]$ module show AllPaths-LG-v49967

module-whatis	 AllPaths-LG v49967
prepend-path	 PATH /opt/software/AllPaths-LG/v49967/bin
prepend-path	 MANPATH /opt/software/AllPaths-LG/v49967/share/doc

[asrini@node062 ~]$ module load AllPaths-LG-v49967

[asrini@node062 ~]$ which AllPathsReport

[asrini@node062 ~]$ AllPathsReport
Performing re-exec to adjust stack size.

Usage: AllPathsReport arg1=value1 arg2=value2 ...

Required arguments:

PRE (String)
DATA (String)
RUN (String)

Optional arguments:

SUBDIR (String) default: test
ASSEMBLY (String) default: final
MIN_CONTIG (int) default: 1000

To see additional special arguments, type: AllPathsReport --help special

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