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Quick start

SPAdes assembler supports:

  • Assembly of second-generation sequencing data (Illumina or IonTorrent);
  • PacBio and Nanopore reads that are used as supplementary data only.

SPAdes allows to assemble genomes, metagenomes, transcriptomes, viral genomes etc.

Current SPAdes version: 4.2.0.

  1. 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.

  2. Test your SPAdes installation by running 

        bin/spades.py --test

Useful one-liners

  • 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

  • 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

  • Assemble a uniformly covered isolate bacterial genome : 

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

  • Assemble a metagenome: 

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

  • Assemble a transcriptome: 

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

  • Assemble an RNA viral genome: 

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

Available assembly modes

  • --isolate - isolate (standard) bacterial data;

  • --sc - single-cell bacterial data;

  • --meta - metagenome assembly;

  • --plasmid / --metaplasmid - plasmid discovery in standard bacterial / metagenomic data;

  • --metaviral - viral assembly from metagenomic data;

  • --rna - transcriptome assembly (RNA-Seq);

  • --rnaviral - assembling viral RNA-Seq data;

  • --bio - assembly of non-ribosomal and polyketide gene clusters;

  • --corona - coronaviridae genome assembly;

  • --sewage - wastewater samples analysis.

Standalone SPAdes tools