SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.

• Version: 4.2.0
• Added: September, 2014
• Updated: May, 2025
• Link: https://github.com/ablab/spades

See versions which are available:

$ module avail spades

Load one version into your environment and run it:

$ module load spades/4.2.0
$ spades.py --help
$ spades.py --test

#!/bin/env bash
#SBATCH -p highmem
#SBATCH -n 8
#SBATCH -J spades

module load spades/3.15

readonly DATADIR=~/data/bfusca
readonly OUTDIR=/var/scratch/aorth-spades-oct8

# create output directory
mkdir -p ${OUTDIR}

# run spades with 8 CPU threads
# run spades with 384 GB of RAM (default is 250, but it ran out of memory before)
spades.py -k 27 -1 ${DATADIR}/1_S1_L001_R1_001_val_1.fastq.gz -2 ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR} -t 8 -m 384

echo
echo "Remember to check (and clean!) output directory on compute07:"
echo
echo "  ${OUTDIR}"

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/ablab/spades/releases/download/v4.2.0/SPAdes-4.2.0-Linux.tar.gz
$ tar xf SPAdes-4.2.0-Linux.tar.gz
$ sudo cp -r SPAdes-4.2.0-Linux /export/apps/spades/4.2.0

Note: if you get the error Exception caught basic_string::_S_construct null not valid you need to call the spades.py script, not the spades binary!