HPC pipeline for parrallel assembly of WGS metagenomes (SLURM)
First, create the needed conda environment from the assembly_env.yml file in config folder.
conda env create -f assembly_env.yml
1- Edit the config.sh file with relevant informations
2- Create a list of file to process (see example_list.txt)
3- Run assembly
This command will read the number of files in the list of files to process and submit an array job accordingly.
./1_run_megahit.sh
4- Run coverage
Once the assemblies are done and complete, coverage for each contig can be obtained running the command:
./2_get_coverage.sh