SPAdes is an assembly toolkit containing various assembly pipelines.

• Complete SPAdes user manual

• SPAdes download page

• Latest SPAdes publication

• Complete user manual can be found here. Information below is provided merely for your convenience and cannot be considered as the user guide.

• SPAdes is an assembler for second-generation sequencing data (Illumina or IonTorrent). PacBio and Nanopore reads are supported only as supplementary data. SPAdes can assemble genomes, metagenomes, transcriptomes, viral genomes etc.

• Download SPAdes binaries for Linux or MacOS. You can also compile SPAdes from source (requires g++ 9.0+, cmake 3.16+, zlib and libbz2). SPAdes requires only Python 3.8+ to be installed.

• Test your SPAdes installation by running

    bin/spades.py --test

• A single paired-end library (separate files, gzipped):

    bin/spades.py -1 left.fastq.gz -2 right.fastq.gz -o output_folder

• A single paired-end library (interlaced reads):

    bin/spades.py --12 interlaced.fastq -o output_folder

• Two paired-end libraries (separate files):

    bin/spades.py --pe1-1 1_left.fastq --pe1-2 1_right.fastq --pe2-1 2_left.fastq --pe2-2 2_right.fastq -o output_folder

• IonTorrent data:

    bin/spades.py --iontorrent -s it_reads.fastq -o output_folder

• A paired-end library coupled with long PacBio reads:

    bin/spades.py -1 left.fastq.gz -2 right.fastq.gz --pacbio pb.fastq -o output_folder

• Available assembly modes: --isolate, --sc, --plasmid, --meta, --metaplasmid, --metaviral, --rna, --rnaviral, --corona, --bio.

If you use SPAdes in your research, please cite our latest paper.

In case you perform hybrid assembly using PacBio or Nanopore reads, you may also cite Antipov et al., 2015. If you use multiple paired-end and/or mate-pair libraries you may additionally cite papers describing SPAdes repeat resolution algorithms Prjibelski et al., 2014 and Vasilinetc et al., 2015.

If you use other pipelines, please cite the following papers:

• metaSPAdes: Nurk et al., 2017.
• plasmidSPAdes: Antipov et al., 2016.
• metaplasmidSPAdes / plasmidVerify: Antipov et al., 2019
• metaviralSPAdes / viralVerify: Antipov et al., 2020
• rnaSPAdes: Bushmanova et al., 2019.
• biosyntheticSPAdes: Meleshko et al., 2019.
• coronaSPAdes paper is currently available at bioRxiv.

You may also include older papers Nurk, Bankevich et al., 2013 or Bankevich, Nurk et al., 2012, especially if you assemble single-cell data.

Please, leave your comments and bug reports at our GitHub repository tracker. If you have any troubles running SPAdes, please attach params.txt and spades.log from the output folder.