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

• Version: 3.15 (3.15.5)
• Added: September, 2014
• Updated: September, 2022
• Link: https://github.com/ablab/spades

See versions of spades which are available:

$ module avail spades

Load one version into your environment and run it:

$ module load spades/3.15
$ spades.py --help
$ spades.py --test

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

module load spades/3.13.0

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

# create output directory
mkdir -p ${OUTDIR}

# run spades with 8 CPUs on mammoth (it has 16 logical CPUs, but only 8 are physical)
# 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/v3.15.5/SPAdes-3.15.5-Linux.tar.gz
$ tar xf SPAdes-3.15.5-Linux.tar.gz
$ sudo mv /export/apps/spades/3.15 /export/apps/spades/3.15.bak
$ sed -i '1s/python/python3/' SPAdes-3.15.5-Linux/bin/spades.py
$ sudo cp -r SPAdes-3.15.5-Linux /export/apps/spades/3.15

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!