Installation

SPAdes requires a 64-bit Linux system or Mac OS and Python (3.8 or higher) to be pre-installed on it. To obtain SPAdes you can either download binaries or download source code and compile it yourself.

In case of successful installation the following files will be placed in the bin directory:

spades.py (main executable script)
metaspades.py (main executable script for metaSPAdes)
plasmidspades.py (main executable script for plasmidSPAdes)
metaplasmidspades.py (main executable script for metaplasmidSPAdes)
metaviralspades.py (main executable script for metaviralSPAdes)
rnaspades.py (main executable script for rnaSPAdes)
rnaviralspades.py (main executable script for rnaviralSPAdes)
coronaspades.py (wrapper script for coronaSPAdes mode)
spades-core (assembly module)
spades-gbuilder (standalone graph builder application)
spades-gmapper (standalone long read to graph aligner)
spades-kmercount (standalone k-mer counting application)
spades-hammer (read error correcting module for Illumina reads)
spades-ionhammer (read error correcting module for IonTorrent reads)
spades-bwa (BWA alignment module which is required for mismatch correction)
spades-corrector-core (mismatch correction module)

Downloading SPAdes Linux binaries

To download SPAdes Linux binaries and extract them, go to the directory in which you wish SPAdes to be installed and run:

    wget https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0-Linux.tar.gz
    tar -xzf SPAdes-4.0.0-Linux.tar.gz
    cd SPAdes-4.0.0-Linux/bin/

In this case you do not need to run any installation scripts - SPAdes is ready to use. We also suggest adding SPAdes installation directory to the PATH variable.

SPAdes Linux binaries are built using ManyLinux 2.28. SPAdes binaries should be compatible with systems using glibc 2.28 and newer including ALT Linux 10+, RHEL 9+, Debian 11+, Fedora 34+, Mageia 8+, Photon OS 3.0 with updates, Ubuntu 21.04+. In case of any problems we recommend building from sources.

Downloading SPAdes binaries for Mac

To obtain SPAdes binaries for Mac, go to the directory in which you wish SPAdes to be installed and run:

    curl https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0-Darwin.tar.gz
    tar -zxf SPAdes-4.0.0-Darwin.tar.gz
    cd SPAdes-4.0.0-Darwin/bin/

Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the PATH variable.

Downloading and compiling SPAdes source code

If you wish to compile SPAdes by yourself you will need the following libraries to be pre-installed:

g++ (version 9 or higher)
cmake (version 3.16 or higher)
zlib
libbz2

If you meet these requirements, you can download the SPAdes source code:

    wget https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0.tar.gz
    tar -xzf SPAdes-4.0.0.tar.gz
    cd SPAdes-4.0.0

and build it with the following script:

    ./spades_compile.sh

SPAdes will be built in the directory ./bin. If you wish to install SPAdes into another directory, you can specify full path of destination folder by running the following command in bash or sh:

    PREFIX=<destination_dir> ./spades_compile.sh

for example:

    PREFIX=/usr/local ./spades_compile.sh

which will install SPAdes into /usr/local/bin.

After installation, you will get the same files (listed above) in bin directory (or <destination_dir>/bin if you specified PREFIX). We also suggest adding bin directory to the PATH environment variable.

Building additional tools

SPAdes toolkit includes a number of standalone tools that are built using core SPAdes algorithms. This includes:

Binning refining tool BinSPreader
HMM-to-graph aligning tool Pathracer
Sequence-to-graph aligning tool SPAligner

These tools are not built by default and therefore must be built separately. One can pass -SPADES_ENABLE_PROJECTS="semicolon-separated list of projects" to enable building only subset of SPAdes components. The components are:

By default, only SPAdes and SPAdes tools are enabled (so -DSPADES_ENABLE_PROJECTS="spades;spades_tools" is the default). Alternatively, one can simply enable building everything via specifying SPADES_ENABLE_PROJECTS="all".

Enabling NCBI SRA input file support

SPAdes can be configured to read NCBI SRA files directly (via NCBI SDK). To enable NCBI SDK support pass -DSPADES_USE_NCBISDK=ON option to spades_compile.sh. This option is disabled by default due to possible compatibility issues. All pre-built release binaries support NCBI SRA input.

Verifying your installation

For testing purposes, SPAdes comes with a toy data set (reads that align to the first 1000 bp of E. coli). To try SPAdes on this data set, run:

    <spades installation dir>/bin/spades.py --test

If you added bin folder from SPAdes installation directory to the PATH variable, you can run:

    spades.py --test

For simplicity we further assume that the bin folder from SPAdes installation directory is added to the PATH variable.

If the installation is successful, you will find the following information at the end of the log:

===== Assembling finished. Used k-mer sizes: 21, 33, 55

 * Corrected reads are in spades_test/corrected/
 * Assembled contigs are in spades_test/contigs.fasta
 * Assembled scaffolds are in spades_test/scaffolds.fasta
 * Assembly graph is in spades_test/assembly_graph.fastg
 * Assembly graph in GFA format is in spades_test/assembly_graph_with_scaffolds.gfa
 * Paths in the assembly graph corresponding to the contigs are in spades_test/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in spades_test/scaffolds.paths

======= SPAdes pipeline finished.

========= TEST PASSED CORRECTLY.

SPAdes log can be found here: spades_test/spades.log

Thank you for using SPAdes!