Newer
Older
Comparing genome and gene reconstruction when using short reads (Illumina), long reads (Oxford Nanopore Technology, ONT)
and a hybrid approach.
# Setup
```bash
git clone --recurse-submodules https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab
```
[About git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules)
TODO: other dependencies ???
# Analysis
## On LCSB HPC server `iris`
Main `conda` environment: `/scratch/users/vgalata/miniconda3/ONT_pilot`
Example commands for `GDB`:
```bash
# conda
conda activate /scratch/users/vgalata/miniconda3/ONT_pilot
# analysis: check which rules will be executed
snakemake -s workflow/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn
# submit jobs using slurm
./config/GDB/sbatch.sh
# report
snakemake -s workflow_report/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn
```
### `conda` environment
If the path specified above does not exists, you can create the environment from `requirements.yaml`
and replace the env. path in `sbatch.sh` files by `"ONT_pilot"`.
```bash
# will create env. ONT_pilot
conda env create -f requirements.yaml