short_read_assembly
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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 –pe1-s Blah_R1_unPairNtrim.fq –pe2-s Blah_R2_unPairNtrim.fq -o Metaspades_Blah_output
##
conda deactivate
short_read_assembly.1567784601.txt.gz · Last modified: by 134.190.234.196