Assembly

Assembly

first i created two directories within my project, flye and raw_data and changed my working directory to raw_data

mkdir flye
mkdir raw_data
cd raw_data

i then created a symbolic link to the black band disease genome read data

ln -s /pvol/data/metagenome_assembly/bbd_0.1.fastq.gz .

i then changed the working directory to flye and ran a shell slurm script (run_flye_bbd.sh) with the following code to assemble the black band disease genome:

#!/bin/bash
#SBATCH --time=720
#SBATCH --ntasks=12 --mem=10gb

echo "Starting flye bbd in $(pwd) at $(date)"

flye --nano-hq ../raw_data/bbd_0.1.fastq.gz --threads 12 --out-dir bbd --meta

echo "Finished flye bbd in $(pwd) at $(date)"

cd ..
cd flye
sbatch run_flye_bbd.sh