The following is a shell example to run metaspades when short reads are available.


#!/bin/bash\\
#$ -S /bin/bash\\
. /etc/profile\\
#$ -cwd\\
#$ -o Blah.log\\
#$ -pe threaded 20\\

cd /to/the/path/containing/the reads/\\
source activate spades\\
metaspades.py -t 20 -m 230 --pe1-1 Blah_R1_PairNtrim.fq --pe1-2 Blah_R2_PairNtrim.fq  --pe-s Blah_R1R2unPairNtrim.fq -o /path/to/Metaspades_Blah_output\\
conda deactivate