About SPAdes

SPAdes - St. Petersburg genome assembler - 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.

SPAdes version 3.15.5 was released under GPLv2 on July 14th, 2022 and can be downloaded here.

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