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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