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