SPAdes (software)

SPAdes, short for the St. Petersburg genome assembler, is a genome assembly algorithm developed by researchers at St. Petersburg State University and St. Petersburg Academic University in Russia together with the University of California, San Diego. It was designed specifically to assemble DNA sequencing data from single bacterial cells and from small multi-cell bacterial samples, a task earlier assembly programs handled poorly because single-cell sequencing produces highly uneven read coverage across the genome, variable insert sizes, and a higher rate of sequencing errors. SPAdes accepts reads from several sequencing platforms, including Illumina, Ion Torrent, PacBio and Oxford Nanopore, and reconstructs them into longer contiguous genomic segments, or contigs, that approximate the original genome sequence. Its de Bruijn graph based approach and error correction steps let it cope with the irregular coverage patterns that single-cell data produces, making it a widely used tool in microbial genomics.