Purdue University

Commands

• coronaspades.py
• metaplasmidspades.py
• metaspades.py
• metaviralspades.py
• plasmidspades.py
• rnaspades.py
• rnaviralspades.py
• spades.py
• spades_init.py
• truspades.py
• spades-bwa
• spades-convert-bin-to-fasta
• spades-core
• spades-corrector-core
• spades-gbuilder
• spades-gmapper
• spades-gsimplifier
• spades-hammer
• spades-ionhammer
• spades-kmer-estimating
• spades-kmercount
• spades-read-filter
• spades-truseq-scfcorrection

Module

You can load the modules by:

module load biocontainers
module load spades 

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run spades on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=spades
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers spades

spades.py --pe1-1 SRR11234553_1.fastq --pe1-2 SRR11234553_2.fastq -o spades_out -t 24