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About SPAdes

SPAdes is a versatile toolkit designed for assembly and analysis of sequencing data. SPAdes is primarily developed for Illumina sequencing data, but can be used for IonTorrent as well. Most of SPAdes pipelines support hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as a supplementary data.

SPAdes package contains assembly pipelines for isolated and single-cell bacterial, as well as metagenomic and transcriptomic data. Additional modes allow to discover bacterial plasmids and RNA viruses, as well as perform HMM-guided assembly. Besides, SPAdes package includes supplementary tools for efficient k-mer counting and k-mer-based read filtering, assembly graph construction and simplification, sequence-to-graph alignment and metagenomic binning refinement.

Current version: see VERSION file.

Quick start

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

Citation

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:

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

Feedback and bug reports

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.