short_read_assembly
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
short_read_assembly.txt · Last modified: by 24.138.68.92