## Short Read WGS assembly using SPades

#!/bin/bash
#SBATCH -e L121spades.err 
#SBATCH -o L121spades.out 
#SBATCH --mem-per-cpu=20G 
#SBATCH -p scavenger
#SBATCH --cpus-per-task=8
#SBATCH --mail-type=ALL --mail-user=[e-mail]

module load SPAdes/3.15.4-rhel8

spades.py -O L121_spades_assembly -1 L121_R1_001.fastq.gz -2 L121_R2_001.fastq.gz\
--TMP_DIR /work/$USER

# Abyss




Initial test on a single lethal line

conda activate
conda activate abyss-env

#!/bin/bash
#SBATCH -e L121abyss.err
#SBATCH -o L121abyss.out
#SBATCH --mem-per-cpu=20G
#SBATCH -p scavenger
#SBATCH --cpus-per-task=4
#SBATCH --mail-type=ALL --mail-user=[e-mail]

conda activate abyss-env

abyss-pe name=L121 k=96 in='L121_R1_001.fastq.gz L121_R2_001.fastq.gz'\
--TMP_DIR /work/$USER

`