About SPAdes

SPAdes - St. Petersburg genome assembler - a versatile toolkit designed for assembling and analyzing sequencing data from Illumina and IonTorrent technologies. In addition, most of SPAdes pipelines support a hybrid mode allowing the use of long reads (PacBio and Oxford Nanopore) as supplementary data.

SPAdes package provides pipelines for DNA assembly of isolates and single-cell bacteria, as well as of metagenomic and transcriptomic data. Additional modes allow to recover bacterial plasmids and RNA viruses, perform HMM-guided assembly and more. SPAdes package also 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.

SPAdes version 4.0.0 was released under GPLv2 on June 3rd, 2024 and can be downloaded here.

The latest SPAdes paper describing various pipelines in a protocol format is available here.