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SPAdes

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

Information

Usage

See versions of spades which are available:

$ module avail spades

Example batch job

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

module load spades/3.6.0

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 mammoth:"
echo
echo "  ${OUTDIR}"

Installation

Notes from the sysadmin during installation:

$ sudo yum install cmake28.x86_64
$ cd /tmp
$ wget http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz
$ tar xf SPAdes-3.5.0.tar.gz
$ cd SPAdes-3.5.0
$ scl enable devtoolset-2 bash
$ sudo mkdir -p /export/apps/spades/3.5.0
$ sudo chown aorth:aorth /export/apps/spades/3.5.0
$ PREFIX=/export/apps/spades/3.5.0 ./spades_compile.sh
$ sudo chown -R root:root /export/apps/spades/3.5.0

Running

After loading the module, consult the built-in help:

$ spades.py --help
spades-software.1471267803.txt.gz · Last modified: 2016/08/15 16:30 by joguya