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/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	3.15.3, 3.15.4, 3.15.5
BELL	3.15.3, 3.15.4, 3.15.5
GAUTSCHI	3.15.3, 3.15.4, 3.15.5
NEGISHI	3.15.3, 3.15.4, 3.15.5
SCHOLAR	3.15.3, 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

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 clusters:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers spades

# Your spades workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers spades

# Your spades workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers spades

# Your spades workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers spades

# Your spades workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers spades

# Your spades workflow...