SPAdes overview
SPAdes is a versatile toolkit designed for the 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 a hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as supplementary data. The package enables the assembly of bacterial isolates, single-cell genomes, metagenomes, and transcriptomes while featuring specialized modules for plasmid and RNA virus recovery. It integrates k-mer-based algorithms for read processing, graph manipulation, and sequence alignment, supporting diverse genomic analyses through a modular pipeline architecture.
Protocol basic steps
- Assembling isolate bacterial datasets
- Assembling metagenomic datasets
- Assembling sets of putative plasmids
- Assembling transcriptomes
- Assembling putative biosynthetic gene clusters
- Installing SPAdes
- Providing input via command line
- Providing input data via YAML format
- Restarting previous run
- Determining strand-specificity of RNA-seq data
| Type | Genome Assembler Toolkit |
| Homepage (Documentation) | SPAdes Assembly Toolkit |
| Source code | SPAdes source code |
| Current version | SPAdes version: 4.0.0. |
| Operating system | SPAdes binaries for Linux or MacOS. |
| Software interface | Command-line user interface |
| Input Data formats | FASTA and FASTQ (can be gzipped) formats. NCBI SRA (binary format). |
| Output Data formats | GFA 1.2 and legacy FASTG formats. |
| Dependencies | Python 3.8 or higher |
| Standalone tools | spades-kmercount; spades-read-filter; spades-kmer-estimating; spades-gbuilder; spades-gsimplifier; spades-gfa-split; spalgner; spades-gmapper; binspreader; pathracer |
| Supported technologies | Illumina or IonTorrent, PacBio and Nanopore |
| Availability | Free and open-source software |
| Maintained and Supported by | SPAdes team |
| License | GPLv2 |
Instructions
Download SPAdes binaries for Linux or MacOS here. 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.
Feedback and bug reports
Please, leave your comments and bug reports at GitHub repository tracker.
Citation and usage
Prjibelski, Andrey, et al. “Using SPAdes De Novo Assembler.” Current Protocols in Bioinformatics, vol. 70, no. 1, June 2020, https://doi.org/10.1002/cpbi.102.
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This information is provided for educational and research purposes only. There is no affiliation, endorsement, or partnership with the tool developers or associated institutions.
