Spades
Introduction
Spades is an assembly toolkit containing various assembly pipelines.
For more information, please check:
BioContainers: https://biocontainers.pro/tools/spades
Home page: https://cab.spbu.ru/software/spades/
Versions
3.15.4
3.15.5
Commands
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
coronaspades.py
metaplasmidspades.py
metaspades.py
metaviralspades.py
plasmidspades.py
rnaspades.py
rnaviralspades.py
spades.py
spades_init.py
truspades.py
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 clusters:
#!/bin/bash
#SBATCH -p PartitionName # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=spades
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module purge
module load spades/XXXX ### you can run *module avail spades* to check all available versions
spades.py --pe1-1 SRR11234553_1.fastq --pe1-2 SRR11234553_2.fastq -o spades_out -t 4