A simple pipeline for reassigning primary contigs that should be labelled as haplotigs.
See which versions of purge_haplotigs are available:
$ module avail purge_haplotigs
Load one version into your environment and run it:
$ module load purge_haplotigs/1.1.1 $ purge_haplotigs test
Note: Please use the ''-t'' option to tell purge_haplotigs how many CPU threads it should use or else it will automatically use four (4). This number should match the number of CPUs you requested in your SLURM batch allocation.
Notes from the sysadmin during installation:
$ cd /tmp $ git clone https://bitbucket.org/mroachawri/purge_haplotigs.git $ git checkout v1.1.1 $ sudo mkdir -p /export/apps/purge_haplotigs/1.1.1 $ sudo cp -r ./* /export/apps/purge_haplotigs/1.1.1 $ sudo chown -R root:root /export/apps/purge_haplotigs/1.1.1