LoRDEC processes data coming from high throughput sequencing machines of the second and third generations. These data are called sequencing reads, or simply reads for short. Technically speaking it processes short reads and long reads to correct errors in the long reads.
See versions which are available:
$ module avail lordec
Load one version into your environment and run it:
$ module load lordec/0.9 $ lordec-correct $ lordec-trim
N.B. Please use the
-T option to set the number of CPU threads for your program. This number should match the number of CPUs you requested from SLURM in your SBATCH job script.
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/lordec-src_0.9.tar.bz2 $ tar xf lordec-src_0.9.tar.bz2 $ cd lordec-src_0.9 $ scl enable devtoolset-7 bash $ sed -i -e 's/cmake/cmake3/' Makefile $ make clean all -j4 $ sudo mkdir -p /export/apps/lordec/0.9/bin $ sudo cp lordec-build-SR-graph lordec-correct lordec_sge_slurm_wrapper.sh lordec-stat lordec-trim lordec-trim-split /export/apps/lordec/0.9/bin $ sudo cp CHANGELOG.md LICENSE README.md /export/apps/lordec/0.9