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An ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.



See which versions of pear are available:

$ module avail pear

Load one version into your environment and run it:

$ module load pear/0.9.6
$ pear

Note: please use the -j option to control how many CPU threads pear uses. This should match the number of CPUs you requested in your SLURM SBATCH job parameters.


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ tar xf pear_0.9.6_src_all.tar.gz
$ cd pear-0.9.6-src
$ scl enable devtoolset-7 bash
$ ./configure --prefix=/export/apps/pear/0.9.6
$ make
$ sudo mkdir -p /export/apps/pear/0.9.6
$ sudo chown aorth /export/apps/pear/0.9.6
$ make install
$ sudo chown -R root:root /export/apps/pear/0.9.6

Note: I downloaded this from galaxyproject because the upstream site requires academic registration and I never received the confirmation mail to download the software. Also, this is the URL that is used by Conda.

pear-software.txt · Last modified: 2020/04/16 11:14 by aorth