README.md

About

Comparing genome and gene reconstruction when using short reads (Illumina), long reads (Oxford Nanopore Technology, ONT) and a hybrid approach.

Setup

git clone --recurse-submodules https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab

About git submodules

TODO: other dependencies ???

Analysis

On LCSB HPC server iris

Main conda environment: /scratch/users/vgalata/miniconda3/ONT_pilot

Example commands for GDB:

# 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".

# will create env. ONT_pilot
conda env create -f requirements.yaml