spades
SPAdes- St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
Detailed usage can be found here: https://github.com/ablab/spades
Link to section 'Versions' of 'spades' Versions
- 3.15.3
- 3.15.4
- 3.15.5
Link to section 'Commands' of 'spades' 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
Link to section 'Module' of 'spades' Module
You can load the modules by:
module load biocontainers
module load spades
Link to section 'Example job' of '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