SPAdes
Introduction
SPAdes
- St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
Detailed usage can be found here: https://github.com/ablab/spades
Versions
3.15.3
3.15.4
3.15.5
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
Warning
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